[Objective] This study was performed to screen functional genes related to the fertility conversion of thermo-sensitive genic male sterile （TGMS） lines of Brassica juncea L. [Method] A B. juncea TGMS line K121S was ...[Objective] This study was performed to screen functional genes related to the fertility conversion of thermo-sensitive genic male sterile （TGMS） lines of Brassica juncea L. [Method] A B. juncea TGMS line K121S was selected as the experimental material. The total RNAs were isolated from fertile and sterile pollens at different development stages, including mother cell stage, tetrad stage, tricellular pollen stage and maturity stage. DDRT-PCR was carried out to identify differentially expressed genes. [Result] A total of 44 differentially expressed cDNA fragments were identified with Dot blot. And seven candidate genes related to fertility conversion of K121S were screened out by BLASTN, including callose synthase gene, aldehyde dehydrogenase gene and RNA polymerase I transcription factor RRN3 gene which were differentially expressed at the transcriptional level, H＇-ATPase gene, fructose diphosphate aldolase -class I gene, teucine-rich repeat receptor-Jike serine/threonine- protein kinase gene and alkaline/neutral invertase gene, which were differentially expressed at the post-transcriptional level. [Conclusion] The results of this study will help to explain the molecular mechanism of thermo-sensitive genic male sterility of B. juncea.展开更多
The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 m...The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.展开更多
The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in fla...The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in flatfish genome have resulted in controversial findings.This study focuses on 18S rRNA genes of the widely distributed tongue sole,Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae),aiming to explore sequence polymorphism.Five distinct 18S rDNA sequence types(Type A,B,R1,R2,and R3)were identified,suggesting a departure from concerted evolution.A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes.The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions.Three types(Type R1,R2,and R3)were identified as recombinants between Type A and B sequences,with simple crossing over and gene conversion as the most likely recombination mechanisms.These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.展开更多
The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops worldwide.However,its genetic origin remains controversial,and its domestication history remains unknown.In this study,we used a range ...The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops worldwide.However,its genetic origin remains controversial,and its domestication history remains unknown.In this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato.The diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to sweetpotato.The tetraploid progenitor of sweetpotato was most likely l.batatas 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast genome.Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome duplication.In addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome conver-sions.Our analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of sweetpotato.This study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.展开更多
Background Infantile proximal spinal muscular atrophy （SMA） is a common autosomal recessive neuromuscular disorder. Approximately 90-95% cases of SMA result from homozygous deletion of survival motor neuron gene 1（...Background Infantile proximal spinal muscular atrophy （SMA） is a common autosomal recessive neuromuscular disorder. Approximately 90-95% cases of SMA result from homozygous deletion of survival motor neuron gene 1（SMN1） and 5% cases are caused by compound heterozygous mutation （a SMN1 deletion on one allele and a subtle mutation on the other allele）.Methods In this research, two unrelated patients were clinically diagnosed according to the criteria of proximal SMA. Genetic diagnosis was performed to detect the homozygous deletion of exon 7 of SMN1 by PCR-restriction fragment length polymorphism （RFLP） and genomic sequencing. Multiplex ligation-dependent probe amplification （MLPA） analysis was carried out to measure copy numbers of SMN1, SMN2 and neuronal apoptosis inhibitor protein （NAIP） in the patients. Further sequencing of SMN1allele-specific PCR （AS-PCR） and SMN1 clones were also performed to analyze the point mutation of SMN1 gene. Additionally,the pedigree analysis of these two families was carried out to identify the transmission of the mutation.Results The inconsistent results using PCR-RFLP and genomic sequencing showed homozygous deletion of exon 7 of SMN1 and heterozygous deletion accompanied with a suspicious mutation in SMN1 gene, respectively. MLPA analysis of these two cases exhibited one SMN1 copy deletion. One identical c.863G〉T （p. Arg288Met） mutation was found in two cases by sequencing the SMN1 clones, which confirmed that both cases were SMA compound heterozygotes. One case showed partial conversion to form hybrid SMN （SMN2 17/SMN1 E8） identified by clones sequencing and another case carrying 3 SMN2 implied complete conversion from SMN1 to SMN2.Conclusion p. Arg288Met is more a disease-causing mutation than a polymorphism variation, and children with this mutation may have more severe phenotypes.展开更多
Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes...Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes.However,a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades.Here,we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels.Our results showed that rodent TLRs were dominated by purifying selection,but a series of positively selected sites(PSSs)primarily located in the ligand-binding domain was also identified.The numbers of PSSs differed among TLRs,and nonviralsensing TLRs had more PSSs than those in viral-sensing TLRs.Gene-conversion events were found between TLR1 and TLR6 in most rodent species.Population genetic analyses showed that TLR2,TLR8,and TLR12 were under positive selection in Rattus norvegicus and R.tanezumi,whereas positive selection also acted on TLR5 and TLR9 in the former species,as well as TLR1 and TLR7 in the latter species.Moreover,we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species.Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.展开更多
基金Supported by National Natural Science Foundation of China(31160289)Rapeseed Industry Construction Program of Department of Agriculture of Yunnan ProvinceFund for Workstation of Academician Guan Chunyun from Department of Science and Technology of Yunnan Province~~
文摘[Objective] This study was performed to screen functional genes related to the fertility conversion of thermo-sensitive genic male sterile （TGMS） lines of Brassica juncea L. [Method] A B. juncea TGMS line K121S was selected as the experimental material. The total RNAs were isolated from fertile and sterile pollens at different development stages, including mother cell stage, tetrad stage, tricellular pollen stage and maturity stage. DDRT-PCR was carried out to identify differentially expressed genes. [Result] A total of 44 differentially expressed cDNA fragments were identified with Dot blot. And seven candidate genes related to fertility conversion of K121S were screened out by BLASTN, including callose synthase gene, aldehyde dehydrogenase gene and RNA polymerase I transcription factor RRN3 gene which were differentially expressed at the transcriptional level, H＇-ATPase gene, fructose diphosphate aldolase -class I gene, teucine-rich repeat receptor-Jike serine/threonine- protein kinase gene and alkaline/neutral invertase gene, which were differentially expressed at the post-transcriptional level. [Conclusion] The results of this study will help to explain the molecular mechanism of thermo-sensitive genic male sterility of B. juncea.
基金supported by the National Basic Research Program of China (No. 2006CB101700)the National High- tech Research and Development Program (No. 2006AA10Z165)the Program for New Century Excellent Talents in Uni-versity of China (No. NCET2005-05- 0502).
文摘The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.
基金The Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract 2021JZ003the Zhoushan Science and Technology Bureau under contract No.2021C21007+1 种基金the Natural Science Foundation of Zhejiang Province under contract Y21C190023the National Natural Science Foundation of China under contract 31272273.
文摘The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in flatfish genome have resulted in controversial findings.This study focuses on 18S rRNA genes of the widely distributed tongue sole,Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae),aiming to explore sequence polymorphism.Five distinct 18S rDNA sequence types(Type A,B,R1,R2,and R3)were identified,suggesting a departure from concerted evolution.A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes.The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions.Three types(Type R1,R2,and R3)were identified as recombinants between Type A and B sequences,with simple crossing over and gene conversion as the most likely recombination mechanisms.These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.
基金This work was funded by the Ministry of Science and Technology of the People's Republic of China(2019YFD1000703 to J.Y.,2019YFD1000704-2 to M.Y.,and 2019YFD1000701-2 to W.F.)the National Natural Science Foundation of China(32300207 to M.Y.,32272228 to M.L.,and 31771854 to H.W.)+5 种基金the"1+9"Open Competition Project of the Sichuan Academy of Agricultural Sciences to select the best candidates(sweetpotato part of 1+9KJGG001 to M.L.)the Chongqing Normal University Foundation(23XLB033 to M.L.)the Shanghai Municipal Afforestation&City Appearance and Environmental Sanitation Administration(G222413 to M.Y.,G222411 to H.W.,G232405 to H.N.,and G242407 to W.F.)the Science and Technology Commission of Shanghai Municipality(22JC1401300 to H.W.)the Youth Innovation Promotion Association CAS(to J.Y.)the Bureau of Science and Technology for Development CAS(KFJ-BRP-017-42 to J.Y.).
文摘The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops worldwide.However,its genetic origin remains controversial,and its domestication history remains unknown.In this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato.The diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to sweetpotato.The tetraploid progenitor of sweetpotato was most likely l.batatas 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast genome.Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome duplication.In addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome conver-sions.Our analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of sweetpotato.This study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.
基金This study was supported by grants from the National Natural Science Foundation of China （No. 81050034） and from the Foundation of Capital Institute of Pediatrics （No.10-B09）.
文摘Background Infantile proximal spinal muscular atrophy （SMA） is a common autosomal recessive neuromuscular disorder. Approximately 90-95% cases of SMA result from homozygous deletion of survival motor neuron gene 1（SMN1） and 5% cases are caused by compound heterozygous mutation （a SMN1 deletion on one allele and a subtle mutation on the other allele）.Methods In this research, two unrelated patients were clinically diagnosed according to the criteria of proximal SMA. Genetic diagnosis was performed to detect the homozygous deletion of exon 7 of SMN1 by PCR-restriction fragment length polymorphism （RFLP） and genomic sequencing. Multiplex ligation-dependent probe amplification （MLPA） analysis was carried out to measure copy numbers of SMN1, SMN2 and neuronal apoptosis inhibitor protein （NAIP） in the patients. Further sequencing of SMN1allele-specific PCR （AS-PCR） and SMN1 clones were also performed to analyze the point mutation of SMN1 gene. Additionally,the pedigree analysis of these two families was carried out to identify the transmission of the mutation.Results The inconsistent results using PCR-RFLP and genomic sequencing showed homozygous deletion of exon 7 of SMN1 and heterozygous deletion accompanied with a suspicious mutation in SMN1 gene, respectively. MLPA analysis of these two cases exhibited one SMN1 copy deletion. One identical c.863G〉T （p. Arg288Met） mutation was found in two cases by sequencing the SMN1 clones, which confirmed that both cases were SMA compound heterozygotes. One case showed partial conversion to form hybrid SMN （SMN2 17/SMN1 E8） identified by clones sequencing and another case carrying 3 SMN2 implied complete conversion from SMN1 to SMN2.Conclusion p. Arg288Met is more a disease-causing mutation than a polymorphism variation, and children with this mutation may have more severe phenotypes.
基金supported by the Major Program of National Natural Science Foundation of China(32090023)the National Key R&D Program of China(2022YFC2601602)Hunan Provincial Natural Science Foundation of China(2023JJ41038).
文摘Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes.However,a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades.Here,we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels.Our results showed that rodent TLRs were dominated by purifying selection,but a series of positively selected sites(PSSs)primarily located in the ligand-binding domain was also identified.The numbers of PSSs differed among TLRs,and nonviralsensing TLRs had more PSSs than those in viral-sensing TLRs.Gene-conversion events were found between TLR1 and TLR6 in most rodent species.Population genetic analyses showed that TLR2,TLR8,and TLR12 were under positive selection in Rattus norvegicus and R.tanezumi,whereas positive selection also acted on TLR5 and TLR9 in the former species,as well as TLR1 and TLR7 in the latter species.Moreover,we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species.Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.
