Alimentary tract duplications are rare congenital lesions normally diagnosed in newborns and children that can occur anywhere from the mouth to the anus and have a reported incidence of approximately 1 in 4500 life bi...Alimentary tract duplications are rare congenital lesions normally diagnosed in newborns and children that can occur anywhere from the mouth to the anus and have a reported incidence of approximately 1 in 4500 life births. Symptoms and clinical presentation vary greatly. The presentation varies according to age and location. The treatment finally is surgical; total resection when possible should be the aim of the intervention. In pediatric surgery minimally invasive surgical procedures became more and more important over the last decades. In consequence the operative procedure on alimentary tract duplications changed in this manner. We review on case reports and clinical reports on minimally invasive surgery in the treatment of alimentary tract duplications, determine the importance of minimally invasive techniques in the treatment of this rare entity and rule out that further studies in the field should be performed.展开更多
Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hyb...Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hybridization bands detected by a repetitive sequence probe, rTRS, were mapped to the ends of all the four chromosomes. Two or three of the bands detected by each of the other 12 probes were also mapped to different chromosomes. The bands detected by the same probe usually occurred in similar locations of different chromosomes. Loci detected by different DNA probes were often similarly arranged on different chromosomes. Chromosomes 8 and 9 showed colinearity of marker loci arrangement indicating a possible common origin. A segment on chromosome 9 was also very similar to the previously reported duplicated fragments on the ends of chromosomes 11 and 12 which were also detected in this study, indicating a likely common origin. Moreover, the various degrees of distributional similarity of the segments suggest a complex relationship among the chromosomes in the evolution of the rice genome. These results support the proposition that chromosome duplication and diversification may be a mechanism for the origin and evolution of the chromosomes in the rice genome.展开更多
Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploi...Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.展开更多
Genes are continually being created by the processes of genome duplication （ohnolog） and gene duplication （paralog）. Whole-genome duplications have been found to be widespread in plant species and play an importan...Genes are continually being created by the processes of genome duplication （ohnolog） and gene duplication （paralog）. Whole-genome duplications have been found to be widespread in plant species and play an important role in plant evolution. Clearly un-overlapping duplicated blocks of whole-genome duplications can be detected in the genome of sequenced rice （Oryza sativa）. Syntenic ohnolog pairs （ohnologues） of the whole-genome duplications in rice were identified based on their syntenic duplicate lines. The paralogs of ohnologues were further scanned using multi-round reciprocal BLAST best-hit searching （E〈e^-14）. The results indicated that an average of 0.55 sister paralogs could be found for every ohnologue in rice. These results suggest that small-scale duplications, as well as whole-genome duplications, play a significant role in the two duplicated rice genomes.展开更多
Background: Alimentary tract duplications (ATDs) are rare congenital anomalies of the gut tube, seen mainly in neonates and infants. Their presentations are often mimicking other conditions, thus posing a diagnostic c...Background: Alimentary tract duplications (ATDs) are rare congenital anomalies of the gut tube, seen mainly in neonates and infants. Their presentations are often mimicking other conditions, thus posing a diagnostic challenge. Surgical treatment is required in all cases. Objective: The aim of this study is to present our experience in the diagnosis and management of this condition. Subjects and Method: We, retrospectively, reviewed 7 duplications in 7 patients and analyzed sex, age, clinical presentation, location, complications, diagnostic work-up, surgical methods and post-operative course. Encountered diagnostic and surgical difficulties were also reviewed in two extremely rare cases. Results: Patients’ age varied between 2 months and 10 years. All duplications were single. Six of them were intra-abdominal and one thoracoabdominal Three ADTs were asymptomatic and discovered during routine X-ray imaging. One ADT involving the cecum was mimicking appendicitis and complicated by recurrent intussusceptions. The thoracoabdominal one proved a surgical challenge as it was a completely isolated ATD. All patients underwent surgery without postoperative complications. We conclude that despite their rarity, ATDs require a high level of clinical suspicion, especially if they are presented as thoracic masses. Appropriate diagnostic investigation of the pediatric patients is always necessary to avoid delay in diagnosis.展开更多
While many plant lineages display remarkable diversity in morphological form,our understanding of how phenotypic diversity,or disparity,arises in relation to genomic evolution over geologic scales remains poorly under...While many plant lineages display remarkable diversity in morphological form,our understanding of how phenotypic diversity,or disparity,arises in relation to genomic evolution over geologic scales remains poorly understood.Here,we investigated the relationship between phenotypic and genomic evolution in the Fagales,a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous.We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives.Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order.Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic,and rates of evolution were highest during the early radiation of the Fagales crown and its major families.These results suggest that Fagales conforms to an“early-burst”model of disparification,with morphospace being filled early in the order's diversification history,and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication.Species diversification appears decoupled from patterns of both phenotypic and genomic evolution,highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.展开更多
The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb fi...The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.展开更多
Dear Editor, Recently, Ren et al. reported an extensive analysis of the incidence of whole genome duplications (WGDs) throughout the evolutionary history of extant angiosperms (Ren et al., 2018). Examining a wealth of...Dear Editor, Recently, Ren et al. reported an extensive analysis of the incidence of whole genome duplications (WGDs) throughout the evolutionary history of extant angiosperms (Ren et al., 2018). Examining a wealth of genomic data (36 complete genomes and 69 transcriptomic datasets) using commonly applied methods, they detected and located 55 WGDs throughout the an giosperm phylogeny.展开更多
Objective:We aim to assess the clinical performance of cell-free fetal DNA(cffDNA)testing for detecting common fetal aneuploidies as well as subchromosomal deletions/duplications and explore the pregnancy decisions in...Objective:We aim to assess the clinical performance of cell-free fetal DNA(cffDNA)testing for detecting common fetal aneuploidies as well as subchromosomal deletions/duplications and explore the pregnancy decisions in screen-positive cases.Methods:A cohort of 19,531 pregnant women was offered cffDNA testing for detection of trisomies 21,18,and 13(T21,T18,and T13);sex chromosome aneuploidies(SCAs);and subchromosomal deletions/duplications.Screen-positive cases were confirmed by karyotyping and single-nucleotide polymorphism array analysis.Results:A total of 47 cases failed the test.The overall screen-positive rate of chromosomal abnormalities was 1.07%(208/19,484),including 57 cases with T21,18 cases with T18,7 cases with T13,106 cases with SCAs,and 20 cases of subchromosomal deletions/duplications.Positive predictive values were 91.30%(42/46),38.46%(5/13),33.33%(2/6),41.33%(31/75),and 27.78%(5/18),respectively.There was no significant difference in the screening of fetal chromosomal aneuploidies in the high-risk group compared with the low-risk group(P>0.05).All of the pregnant women who had confirmed fetal T21,T18,or T13 terminated their pregnancies,except for a case of T13 mosaic,whereas 45.16%(14/31)of women with fetal SCAs continued their pregnancies.Furthermore,17 pregnant women with positive screens for T21,T18,or T13 without a subsequent diagnosis chose to terminate their pregnancy,whereas 29 of 31 women with SCAs chose to continue their pregnancies.Conclusions:CffDNA testing exhibited good screening accuracy for T21,T18,and T13 and also contributed to detecting fetal SCAs and subchromosomal deletions/duplications.Pregnant women with fetal 47,XXX or 47,XYY were more willing to terminate their pregnancy than those with fetal 45,X or 47,XXY.展开更多
Anthocyanin biosynthesis in plants is spatiotemporally controlled by a suite of transcription factors,with MYB proteins playing a key regulatory role.However,the evolution of the distinct roles of MYB paralogs remains...Anthocyanin biosynthesis in plants is spatiotemporally controlled by a suite of transcription factors,with MYB proteins playing a key regulatory role.However,the evolution of the distinct roles of MYB paralogs remains poorly understood.Our previous studies have established GmMYBA2 and GmMYBA3 as the regulators of seed coat and floral anthocyanin production in soybean(Glycine max),respectively.In this study,we reveal the functional divergence of their paralog GmMYBA1 in orchestrating light-responsive anthocyanin biosynthesis in juvenile tissues and stems.In brief,hypocotyl/stem-and young leaf-predominant expression of GmMYBA1 correlates with photoprotective anthocyanin accumulation.Ectopic overexpression of GmMYBA1 induces systemic pigmentation across leaves,stems,and reproductive organs,whereas RNAi-mediated silencing of GmMYBA1 significantly reduces anthocyanin accumulation in the hypocotyl.Light-dark shift assays confirmed that GmMYBA1 is required for hypocotyl pigmentation,while dual-luciferase assays revealed the specific regulation of the GmMYBA paralogs by GmSTF1/2(soybean TGACG-motif binding factor 1/2).GmSTF1/2 both activate GmMYBA1,with only GmSTF2 weakly inducing GmMYBA2 and neither affecting GmMYBA3.Further investigation indicated that the differential transactivation of GmMYBA promoters largely resulted from their cis-element difference,suggesting regulatory divergence as a driver of MYB paralog diversification.Our findings position GmMYBA1 as the central MYB activator integrating light signaling with anthocyanin biosynthesis,with paralog specialization reflecting evolutionary subfunctionalization post-gene duplication.展开更多
BACKGROUND Complement-mediated thrombotic microangiopathy(TMA)is a rare endothelial injury syndrome caused by dysregulated activation of the alternative complement pathway,often linked to genetic abnormalities in comp...BACKGROUND Complement-mediated thrombotic microangiopathy(TMA)is a rare endothelial injury syndrome caused by dysregulated activation of the alternative complement pathway,often linked to genetic abnormalities in complement factor H(CFH),complement factor I,or complement factor H-related(CFHR)proteins.Both renal transplantation and pregnancy are independent triggers for recurrence.This case highlights a genetically high-risk patient who achieved a successful term pregnancy after renal transplantation without complement inhibition,emphasizing individualized risk stratification,close surveillance,and multidisciplinary management for favourable maternal and graft outcomes.CASE SUMMARY A 32-year-old woman with end-stage renal disease secondary to genetically confirmed complement-mediated TMA—homozygous CFH exon 17 deletion and CFHR3-CFHR1 duplication—was maintained on dialysis for 2.5 years before undergoing a successful live-donor kidney transplant from her mother.Post-transplant immunosuppression included tacrolimus,mycophenolate mofetil,and prednisolone,later modified to azathioprine during pregnancy planning.One-year post-transplant,she conceived spontaneously.Pregnancy was complicated by transient gestational hypertension,controlled with nifedipine,labetalol,and amlodipine.Proteinuria remained<150 mg/day;white blood cell counts 5.8-7.2×109/L without cytopenia.Serum creatinine ranged 0.9-1.1 mg/dL,and tacrolimus trough levels 5-7 ng/mL.At 36 weeks,she delivered a healthy 3 kg infant by elective caesarean section.Postpartum follow-up at three months confirmed stable maternal and graft function.CONCLUSION High-risk complement-mediated TMA patients can achieve successful pregnancy post-transplant through individualized care without mandatory complement blockade.展开更多
Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of re...Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We per- formed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene dupli- cation events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approx- imately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.展开更多
The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants.Most members of the Cucurbitaceae,a family containing^1000 spec...The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants.Most members of the Cucurbitaceae,a family containing^1000 species and many important crops,are climbers and have characteristic tendrils and pepo fruits.Here,we present 127 newly sequenced transcdptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades.We analyzed whole-genome duplication,diversification dynamics,and ancestral morphologies,and found that after early genome duplication event(s),a burst of diversification and morphological innovations in flower,fruit,and root characters occurred under the climate optimum in the Early Eocene.Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80%of cucurbits.We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family.Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals.Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.展开更多
Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene co...Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the origi- nally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.展开更多
The human genome contains millions of DNA regulatory elements and a large number of gene clusters,most of which have not been tested experimentally.The clustered regularly interspaced short palindromic repeats(CRISPR)...The human genome contains millions of DNA regulatory elements and a large number of gene clusters,most of which have not been tested experimentally.The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated nuclease 9(Cas9)programed with a synthetic single-guide RNA(sgRNA)emerges as a method for genome editing in virtually any organisms.Here we report that targeted DNA fragment inversions and duplications could easily be achieved in human and mouse genomes by CRISPR with two sgRNAs.Specifically,we found that,in cultured human cells and mice,efficient precise inversions of DNA fragments ranging in size froma few tens of bp to hundreds of kb could be generated.In addition,DNA fragment duplications and deletions could also be generated by CRISPR through trans-allelic recombination between the Cas9-induced double-strand breaks(DSBs)on two homologous chromosomes(chromatids).Moreover,junctions of combinatorial inversions and duplications of the protocadherin(Pcdh)gene clusters induced by Cas9 with four sgRNAs could be detected.In mice,we obtained founders with alleles of precise inversions,duplications,and deletions of DNA fragments of variable sizes by CRISPR.Interestingly,we found that very efficient inversions were mediated by microhomology-mediated end joining(MMEJ)through short inverted repeats.We showed for the first time that DNA fragment inversions could be transmitted through germlines in mice.Finally,we applied this CRISPR method to a regulatory element of the Pcdha cluster and found a new role in the regulation of members of the Pcdhg cluster.This simple and efficient method should be useful in manipulating mammalian genomes to study millions of regulatory DNA elements as well as vast numbers of gene clusters.展开更多
Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for e...Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.展开更多
Solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal plants.Several sequenced Solanaceae genomes show evidence for wholegenome duplication(WGD),pr...Solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal plants.Several sequenced Solanaceae genomes show evidence for wholegenome duplication(WGD),providing an excellent opportunity to investigate WGD and its impacts.Here,we generated 93 transcriptomes/genomes and combined them with 87 public datasets,for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes.Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades.The Solanaceae tree supports four previously recognized subfamilies(Goetzeioideae,Cestroideae,Nicotianoideae,and Solanoideae)and the designation of three other subfamilies(Schizanthoideae,Schwenckioideae,and Petunioideae),with the placement of several previously unassigned genera.We placed a Solanaceae-specific whole-genome triplication(WGT1)at81 million years ago(mya),before the divergence of Schizanthoideae from other Solanaceae subfamilies at73 mya.In addition,we detected two gene duplication bursts(GDBs)supporting proposed WGD events and four other GDBs.An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene(sub)families revealed that 21 gene clades have retained gene duplicates.These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development.This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development,providing an improved understanding of Solanaceae evolution.展开更多
Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independentl...Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated.Here,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae species.Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the RBGD.We also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of Triticeae.Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat.Moreover,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat.Our results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.展开更多
文摘Alimentary tract duplications are rare congenital lesions normally diagnosed in newborns and children that can occur anywhere from the mouth to the anus and have a reported incidence of approximately 1 in 4500 life births. Symptoms and clinical presentation vary greatly. The presentation varies according to age and location. The treatment finally is surgical; total resection when possible should be the aim of the intervention. In pediatric surgery minimally invasive surgical procedures became more and more important over the last decades. In consequence the operative procedure on alimentary tract duplications changed in this manner. We review on case reports and clinical reports on minimally invasive surgery in the treatment of alimentary tract duplications, determine the importance of minimally invasive techniques in the treatment of this rare entity and rule out that further studies in the field should be performed.
文摘Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hybridization bands detected by a repetitive sequence probe, rTRS, were mapped to the ends of all the four chromosomes. Two or three of the bands detected by each of the other 12 probes were also mapped to different chromosomes. The bands detected by the same probe usually occurred in similar locations of different chromosomes. Loci detected by different DNA probes were often similarly arranged on different chromosomes. Chromosomes 8 and 9 showed colinearity of marker loci arrangement indicating a possible common origin. A segment on chromosome 9 was also very similar to the previously reported duplicated fragments on the ends of chromosomes 11 and 12 which were also detected in this study, indicating a likely common origin. Moreover, the various degrees of distributional similarity of the segments suggest a complex relationship among the chromosomes in the evolution of the rice genome. These results support the proposition that chromosome duplication and diversification may be a mechanism for the origin and evolution of the chromosomes in the rice genome.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA19050404)National Natural Science Foundation of China(No.31800174).
文摘Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.
基金the National NaturalSciencc Foundation of China (90208022,30471067) IBM Shared University Research (LifeScience).
文摘Genes are continually being created by the processes of genome duplication （ohnolog） and gene duplication （paralog）. Whole-genome duplications have been found to be widespread in plant species and play an important role in plant evolution. Clearly un-overlapping duplicated blocks of whole-genome duplications can be detected in the genome of sequenced rice （Oryza sativa）. Syntenic ohnolog pairs （ohnologues） of the whole-genome duplications in rice were identified based on their syntenic duplicate lines. The paralogs of ohnologues were further scanned using multi-round reciprocal BLAST best-hit searching （E〈e^-14）. The results indicated that an average of 0.55 sister paralogs could be found for every ohnologue in rice. These results suggest that small-scale duplications, as well as whole-genome duplications, play a significant role in the two duplicated rice genomes.
文摘Background: Alimentary tract duplications (ATDs) are rare congenital anomalies of the gut tube, seen mainly in neonates and infants. Their presentations are often mimicking other conditions, thus posing a diagnostic challenge. Surgical treatment is required in all cases. Objective: The aim of this study is to present our experience in the diagnosis and management of this condition. Subjects and Method: We, retrospectively, reviewed 7 duplications in 7 patients and analyzed sex, age, clinical presentation, location, complications, diagnostic work-up, surgical methods and post-operative course. Encountered diagnostic and surgical difficulties were also reviewed in two extremely rare cases. Results: Patients’ age varied between 2 months and 10 years. All duplications were single. Six of them were intra-abdominal and one thoracoabdominal Three ADTs were asymptomatic and discovered during routine X-ray imaging. One ADT involving the cecum was mimicking appendicitis and complicated by recurrent intussusceptions. The thoracoabdominal one proved a surgical challenge as it was a completely isolated ATD. All patients underwent surgery without postoperative complications. We conclude that despite their rarity, ATDs require a high level of clinical suspicion, especially if they are presented as thoracic masses. Appropriate diagnostic investigation of the pediatric patients is always necessary to avoid delay in diagnosis.
基金funded by the and the Science and Technology Basic Resources Investigation Program of China(2019FY100900)the Major Program for Basic Research Project of Yunnan Province(202401BC070001)+3 种基金the Yunnan Revitalization Talent Support Program:Yunling Scholar Project,the National Natural Science Foundation of China[key international(regional)cooperative research project no.31720103903]funding from the CAS President's International Fellowship Initiative(no.2020PB0009)the China Postdoctoral Science Foundation(CPSF)International Postdoctoral Exchange Programsupport from the United States National Science Foundation(DEB 1917146 and DBI 1930030)。
文摘While many plant lineages display remarkable diversity in morphological form,our understanding of how phenotypic diversity,or disparity,arises in relation to genomic evolution over geologic scales remains poorly understood.Here,we investigated the relationship between phenotypic and genomic evolution in the Fagales,a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous.We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives.Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order.Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic,and rates of evolution were highest during the early radiation of the Fagales crown and its major families.These results suggest that Fagales conforms to an“early-burst”model of disparification,with morphospace being filled early in the order's diversification history,and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication.Species diversification appears decoupled from patterns of both phenotypic and genomic evolution,highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.
基金This study was supported by the National Natural Science Foundation of China(NSFC,nos.31770331 and 31970318)Guangdong Basic and Applied Basic Research Foundation(no.2020B1515120023).
文摘The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.
文摘Dear Editor, Recently, Ren et al. reported an extensive analysis of the incidence of whole genome duplications (WGDs) throughout the evolutionary history of extant angiosperms (Ren et al., 2018). Examining a wealth of genomic data (36 complete genomes and 69 transcriptomic datasets) using commonly applied methods, they detected and located 55 WGDs throughout the an giosperm phylogeny.
基金supported by the Shanghai Municipal Health Bureau(grants 20174Y0199 and 201740096)Shanghai Clinical and Medical Center of Key Programs(2017ZZ01016)。
文摘Objective:We aim to assess the clinical performance of cell-free fetal DNA(cffDNA)testing for detecting common fetal aneuploidies as well as subchromosomal deletions/duplications and explore the pregnancy decisions in screen-positive cases.Methods:A cohort of 19,531 pregnant women was offered cffDNA testing for detection of trisomies 21,18,and 13(T21,T18,and T13);sex chromosome aneuploidies(SCAs);and subchromosomal deletions/duplications.Screen-positive cases were confirmed by karyotyping and single-nucleotide polymorphism array analysis.Results:A total of 47 cases failed the test.The overall screen-positive rate of chromosomal abnormalities was 1.07%(208/19,484),including 57 cases with T21,18 cases with T18,7 cases with T13,106 cases with SCAs,and 20 cases of subchromosomal deletions/duplications.Positive predictive values were 91.30%(42/46),38.46%(5/13),33.33%(2/6),41.33%(31/75),and 27.78%(5/18),respectively.There was no significant difference in the screening of fetal chromosomal aneuploidies in the high-risk group compared with the low-risk group(P>0.05).All of the pregnant women who had confirmed fetal T21,T18,or T13 terminated their pregnancies,except for a case of T13 mosaic,whereas 45.16%(14/31)of women with fetal SCAs continued their pregnancies.Furthermore,17 pregnant women with positive screens for T21,T18,or T13 without a subsequent diagnosis chose to terminate their pregnancy,whereas 29 of 31 women with SCAs chose to continue their pregnancies.Conclusions:CffDNA testing exhibited good screening accuracy for T21,T18,and T13 and also contributed to detecting fetal SCAs and subchromosomal deletions/duplications.Pregnant women with fetal 47,XXX or 47,XYY were more willing to terminate their pregnancy than those with fetal 45,X or 47,XXY.
基金supported by the Department of Science and Technology of Jilin Province(20220508112RC).
文摘Anthocyanin biosynthesis in plants is spatiotemporally controlled by a suite of transcription factors,with MYB proteins playing a key regulatory role.However,the evolution of the distinct roles of MYB paralogs remains poorly understood.Our previous studies have established GmMYBA2 and GmMYBA3 as the regulators of seed coat and floral anthocyanin production in soybean(Glycine max),respectively.In this study,we reveal the functional divergence of their paralog GmMYBA1 in orchestrating light-responsive anthocyanin biosynthesis in juvenile tissues and stems.In brief,hypocotyl/stem-and young leaf-predominant expression of GmMYBA1 correlates with photoprotective anthocyanin accumulation.Ectopic overexpression of GmMYBA1 induces systemic pigmentation across leaves,stems,and reproductive organs,whereas RNAi-mediated silencing of GmMYBA1 significantly reduces anthocyanin accumulation in the hypocotyl.Light-dark shift assays confirmed that GmMYBA1 is required for hypocotyl pigmentation,while dual-luciferase assays revealed the specific regulation of the GmMYBA paralogs by GmSTF1/2(soybean TGACG-motif binding factor 1/2).GmSTF1/2 both activate GmMYBA1,with only GmSTF2 weakly inducing GmMYBA2 and neither affecting GmMYBA3.Further investigation indicated that the differential transactivation of GmMYBA promoters largely resulted from their cis-element difference,suggesting regulatory divergence as a driver of MYB paralog diversification.Our findings position GmMYBA1 as the central MYB activator integrating light signaling with anthocyanin biosynthesis,with paralog specialization reflecting evolutionary subfunctionalization post-gene duplication.
文摘BACKGROUND Complement-mediated thrombotic microangiopathy(TMA)is a rare endothelial injury syndrome caused by dysregulated activation of the alternative complement pathway,often linked to genetic abnormalities in complement factor H(CFH),complement factor I,or complement factor H-related(CFHR)proteins.Both renal transplantation and pregnancy are independent triggers for recurrence.This case highlights a genetically high-risk patient who achieved a successful term pregnancy after renal transplantation without complement inhibition,emphasizing individualized risk stratification,close surveillance,and multidisciplinary management for favourable maternal and graft outcomes.CASE SUMMARY A 32-year-old woman with end-stage renal disease secondary to genetically confirmed complement-mediated TMA—homozygous CFH exon 17 deletion and CFHR3-CFHR1 duplication—was maintained on dialysis for 2.5 years before undergoing a successful live-donor kidney transplant from her mother.Post-transplant immunosuppression included tacrolimus,mycophenolate mofetil,and prednisolone,later modified to azathioprine during pregnancy planning.One-year post-transplant,she conceived spontaneously.Pregnancy was complicated by transient gestational hypertension,controlled with nifedipine,labetalol,and amlodipine.Proteinuria remained<150 mg/day;white blood cell counts 5.8-7.2×109/L without cytopenia.Serum creatinine ranged 0.9-1.1 mg/dL,and tacrolimus trough levels 5-7 ng/mL.At 36 weeks,she delivered a healthy 3 kg infant by elective caesarean section.Postpartum follow-up at three months confirmed stable maternal and graft function.CONCLUSION High-risk complement-mediated TMA patients can achieve successful pregnancy post-transplant through individualized care without mandatory complement blockade.
文摘Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We per- formed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene dupli- cation events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approx- imately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.
基金This work was supported by the National Natural Science Foundation of China(grant no.31770242 and 31970224).
文摘The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants.Most members of the Cucurbitaceae,a family containing^1000 species and many important crops,are climbers and have characteristic tendrils and pepo fruits.Here,we present 127 newly sequenced transcdptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades.We analyzed whole-genome duplication,diversification dynamics,and ancestral morphologies,and found that after early genome duplication event(s),a burst of diversification and morphological innovations in flower,fruit,and root characters occurred under the climate optimum in the Early Eocene.Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80%of cucurbits.We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family.Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals.Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.
文摘Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the origi- nally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.
基金supported by grants to Q.W.from the National Natural Science Foundation of China(31171015 and 31470820)the Science and Technology Commission of Shanghai Municipality(13XD1402000 and 14JC1403600).
文摘The human genome contains millions of DNA regulatory elements and a large number of gene clusters,most of which have not been tested experimentally.The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated nuclease 9(Cas9)programed with a synthetic single-guide RNA(sgRNA)emerges as a method for genome editing in virtually any organisms.Here we report that targeted DNA fragment inversions and duplications could easily be achieved in human and mouse genomes by CRISPR with two sgRNAs.Specifically,we found that,in cultured human cells and mice,efficient precise inversions of DNA fragments ranging in size froma few tens of bp to hundreds of kb could be generated.In addition,DNA fragment duplications and deletions could also be generated by CRISPR through trans-allelic recombination between the Cas9-induced double-strand breaks(DSBs)on two homologous chromosomes(chromatids).Moreover,junctions of combinatorial inversions and duplications of the protocadherin(Pcdh)gene clusters induced by Cas9 with four sgRNAs could be detected.In mice,we obtained founders with alleles of precise inversions,duplications,and deletions of DNA fragments of variable sizes by CRISPR.Interestingly,we found that very efficient inversions were mediated by microhomology-mediated end joining(MMEJ)through short inverted repeats.We showed for the first time that DNA fragment inversions could be transmitted through germlines in mice.Finally,we applied this CRISPR method to a regulatory element of the Pcdha cluster and found a new role in the regulation of members of the Pcdhg cluster.This simple and efficient method should be useful in manipulating mammalian genomes to study millions of regulatory DNA elements as well as vast numbers of gene clusters.
基金supported by the National Natural Science Foundation of China(31972866)the Strategic Priority Research Program(XDB31000000)supported by the Wuhan Branch,Supercomputing Center,Chinese Academy of Sciences,China。
文摘Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.
基金supported by funds from the National Natural Science Foundation of China(grant nos.31770242,31970224,and 32270232)the Key Laboratory of Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering at Fudan University,and Eberly College of Science and the Huck Institutes of the Life Sciences at the Pennsylvania State University.
文摘Solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal plants.Several sequenced Solanaceae genomes show evidence for wholegenome duplication(WGD),providing an excellent opportunity to investigate WGD and its impacts.Here,we generated 93 transcriptomes/genomes and combined them with 87 public datasets,for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes.Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades.The Solanaceae tree supports four previously recognized subfamilies(Goetzeioideae,Cestroideae,Nicotianoideae,and Solanoideae)and the designation of three other subfamilies(Schizanthoideae,Schwenckioideae,and Petunioideae),with the placement of several previously unassigned genera.We placed a Solanaceae-specific whole-genome triplication(WGT1)at81 million years ago(mya),before the divergence of Schizanthoideae from other Solanaceae subfamilies at73 mya.In addition,we detected two gene duplication bursts(GDBs)supporting proposed WGD events and four other GDBs.An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene(sub)families revealed that 21 gene clades have retained gene duplicates.These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development.This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development,providing an improved understanding of Solanaceae evolution.
基金Wethank the National Natural Science Foundation of China(Grant number 31870209)the Key Science and Technology Program of Henan Prov-ince(201300110800)for research funding.
文摘Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated.Here,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae species.Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the RBGD.We also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of Triticeae.Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat.Moreover,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat.Our results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.
