Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cot...Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cotton production.Genome editing technology,specifically with clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)tools,has opened new possibilities for trait development in cotton.It allows pre-cise and efficient manipulation within the cotton genome when compared with other genetic engineering tools.Current developments in CRISPR/Cas technology,including prime editing,base editing,and multiplexing editing,have expanded the scope of traits in cotton breeding that can be targeted.CRISPR/Cas genome editing has been employed to generate effectively CRISPRized cotton plants with enhanced agronomic traits,including fiber yield and quality,oil improvement,stress resistance,and enhanced nutrition.Here we summarized the various target genes within the cotton genome which have been successfully altered with CRISPR/Cas tools.However,some challenges remain,cotton is tetraploid genome having redundant gene sets and homologs making challenges for genome edit-ing.To ensure specificity and avoiding off-target effects,we need to optimize various parameters such as target site,guide RNA design,and choosing right Cas variants.We outline the future prospects of CRISPR/Cas in cotton breeding,suggesting areas for further research and innovation.A combination of speed breeding and CRISPR/Cas might be useful for fastening trait development in cotton.The potentials to create customized cotton cultivars with enhanced traits to meet the higher demands for the agriculture and textile industry.展开更多
Complex congenital disorders may be caused by multiple genetic alterations and/or environmental hazards. Diagnosis and management of these diseases are usually difficult. Robust next-generation sequencing （NGS） tech...Complex congenital disorders may be caused by multiple genetic alterations and/or environmental hazards. Diagnosis and management of these diseases are usually difficult. Robust next-generation sequencing （NGS） technologies provide unprecedented opportunities to maximize mutation detection and improve genetic counseling and clinical management. Targeted or whole exome sequencing （WES） mainly detects protein-coding DNA sequence aberrations and is the major DNA sequencing technology that is entering clinical practice （Liu et al., 2014）.展开更多
Dear Editor,Obtaining foreign DNA-free crops after genome editing is essential for agricultural applications,because of the current regulatory policies on gene-edited plants in various countries.However,it is usually ...Dear Editor,Obtaining foreign DNA-free crops after genome editing is essential for agricultural applications,because of the current regulatory policies on gene-edited plants in various countries.However,it is usually a time-consuming and labor-consuming process to select and confirm foreign DNA-free offspring,especially in woody plants with long-term life cycles and crop species with complex genomes or T-DNA multisite insertions during genome editing.展开更多
Over the past 20 years,tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of...Over the past 20 years,tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of nonvascular plants to those of flowering plants.However,complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity,highly repetitive sequences,or high ploidy characteristics of complex genomes.Herein,we summarize the challenges of and advances in complex plant genome assembly,including feasible experimental strategies,upgrades to sequencing technology,existing assembly methods,and different phasing algorithms.Moreover,we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes.Finally,we expect that the accurate,gapless,telomere-totelomere,and fully phased assembly of complex plant genomes could soon become routine.展开更多
Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a g...Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a giant ciliated protist,Stentor roeselii,provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species.As a main result,we have unveiled a previously undetected ancient WGD event shaping the genome of its congener,Stentor coeruleus,a model protist used in cytological and evolutionary studies.Genomes of two congeners,S.coeruleus and S.roeselii,are compared and analyzed,revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%)than does S.roeselii,and in S.coeruleus,75%of genes that have a RBH hit in S.roeselii,have paralogs with high amino-acid identity,consistent with a WGD event in the lineage leading to S.coeruleus;(ii)the S.roeselii genome possesses extremely short intergenic regions,implying that the lengths of intergenic regions are under strong selection;(iii)the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv)gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa,possibly relating to the remarkable regenerative ability in Stentor.This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.展开更多
Rapid advances in sequencing and bioinformatics have profoundly enhanced disease understanding[1],while integrated genomic analyses reveal regulatory networks governing biological processes[2].However,research remains...Rapid advances in sequencing and bioinformatics have profoundly enhanced disease understanding[1],while integrated genomic analyses reveal regulatory networks governing biological processes[2].However,research remains disproportionately focused on populations of European ancestry or other groups with large sample sizes,such as Han Chinese,leaving many ethnically diverse and underrepresented populations disadvantaged in genomic medicine[3].Complex human demographic processes influence allele frequencies,define gene sets under selective constraints,and inform variant-filtering strategies crucial for genetic disease diagnosis and genetic counseling.This imbalance limits the global applicability of genomic findings and exacerbates existing health disparities.By prioritizing high-quality genome sequencing from underrepresented populations,researchers can uncover novel genetic variants,refine disease risk predictions,and promote equitable access to precision medicine.展开更多
Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improveme...Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.展开更多
Recent developments in PacBio high-fidelity(HiFi)sequencing technologies have transformed genomic research,with circular consensus se-quencing now achieving 99.9%accuracy for long(up to 25 kb)single-molecule reads.Thi...Recent developments in PacBio high-fidelity(HiFi)sequencing technologies have transformed genomic research,with circular consensus se-quencing now achieving 99.9%accuracy for long(up to 25 kb)single-molecule reads.This method circumvents biases intrinsic to amplification-based approaches,enabling thorough analysis of complex genomic regions including tandem repeats,segmental duplications,ribosomal DNA(rDNA)arrays,and centromeresl as well as direct detection of base modifications,furnishing both sequence and epigenetic data concurrently.This has streamlined a number of tasks including genome assembly,variant detection,and full-length transcript analysis.This review provides a comprehensive overview of the applications and challenges of HiFi sequencing across various fields,including genomics,transcriptomics,and epigenetics.By delineating the evolving landscape of HiFi sequencing in multi-omics research,we highlight its potential to deepen our under-standingofgeneticmechanisms and to advance precision medicine.展开更多
The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1...The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1–5].This innovative sequencing technology stands out due to its ability to generate long sequencing reads,which are pivotal in resolving complex microbial genomic structures that short-read sequencing often fails to address[2,6].展开更多
Diversity array technology （DART^TM） was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice （Oryza sativa L.）genotyping in a high th...Diversity array technology （DART^TM） was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice （Oryza sativa L.）genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc （Numerical taxonomy system for cluster and ordination analysis, v. 2.02j） software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple sequence repeats genotyping outline and varieties＇ pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.展开更多
文摘Cotton(Gossypium hirsutum L.)is one of the most important global crops that supports the textile industry and pro-vides a living for millions of farmers.The constantly increasing demand needs a significant rise in cotton production.Genome editing technology,specifically with clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)tools,has opened new possibilities for trait development in cotton.It allows pre-cise and efficient manipulation within the cotton genome when compared with other genetic engineering tools.Current developments in CRISPR/Cas technology,including prime editing,base editing,and multiplexing editing,have expanded the scope of traits in cotton breeding that can be targeted.CRISPR/Cas genome editing has been employed to generate effectively CRISPRized cotton plants with enhanced agronomic traits,including fiber yield and quality,oil improvement,stress resistance,and enhanced nutrition.Here we summarized the various target genes within the cotton genome which have been successfully altered with CRISPR/Cas tools.However,some challenges remain,cotton is tetraploid genome having redundant gene sets and homologs making challenges for genome edit-ing.To ensure specificity and avoiding off-target effects,we need to optimize various parameters such as target site,guide RNA design,and choosing right Cas variants.We outline the future prospects of CRISPR/Cas in cotton breeding,suggesting areas for further research and innovation.A combination of speed breeding and CRISPR/Cas might be useful for fastening trait development in cotton.The potentials to create customized cotton cultivars with enhanced traits to meet the higher demands for the agriculture and textile industry.
基金supported by the grants from the National High Technology Research and Development Program of China (863 Program) (No. 2012AA02A201)the Tianjin Natural Science Foundation (No. 13JCQNJC10400)
文摘Complex congenital disorders may be caused by multiple genetic alterations and/or environmental hazards. Diagnosis and management of these diseases are usually difficult. Robust next-generation sequencing （NGS） technologies provide unprecedented opportunities to maximize mutation detection and improve genetic counseling and clinical management. Targeted or whole exome sequencing （WES） mainly detects protein-coding DNA sequence aberrations and is the major DNA sequencing technology that is entering clinical practice （Liu et al., 2014）.
基金supported by the National Natural Science Foundation of China(grant nos.32130031 and 31991201)and the China Postdoctoral Science Foundation(grant no.2021M702524).
文摘Dear Editor,Obtaining foreign DNA-free crops after genome editing is essential for agricultural applications,because of the current regulatory policies on gene-edited plants in various countries.However,it is usually a time-consuming and labor-consuming process to select and confirm foreign DNA-free offspring,especially in woody plants with long-term life cycles and crop species with complex genomes or T-DNA multisite insertions during genome editing.
基金supported by the National Natural Science Foundation of China(Grant No.32222019)the National Key R&D Program of China(Grant No.2021YFF1000900).
文摘Over the past 20 years,tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of nonvascular plants to those of flowering plants.However,complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity,highly repetitive sequences,or high ploidy characteristics of complex genomes.Herein,we summarize the challenges of and advances in complex plant genome assembly,including feasible experimental strategies,upgrades to sequencing technology,existing assembly methods,and different phasing algorithms.Moreover,we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes.Finally,we expect that the accurate,gapless,telomere-totelomere,and fully phased assembly of complex plant genomes could soon become routine.
基金supported by the Science & Technology Innovation Project of Laoshan Laboratory(LSKJ202203203)the National Science Foundation of China (32270558)+4 种基金the National Institutes of Health Grant (R35-GM122566-01)the National Science Foundation (DEB-1927159, DBI-2119963)the Moore and Simons Foundations (735927)the Young Taishan Scholar Program of Shandong Provincethe Project of Outstanding Young Innovative Team in Higher Education Institutions of Shandong Province (2023KJ038).
文摘Whole-genome duplication(WGD)events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms.In the present study,the newly sequenced genome of a giant ciliated protist,Stentor roeselii,provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species.As a main result,we have unveiled a previously undetected ancient WGD event shaping the genome of its congener,Stentor coeruleus,a model protist used in cytological and evolutionary studies.Genomes of two congeners,S.coeruleus and S.roeselii,are compared and analyzed,revealing that:(i)the former exhibits a much higher retention rate of colinear-gene pairs(28%)than does S.roeselii,and in S.coeruleus,75%of genes that have a RBH hit in S.roeselii,have paralogs with high amino-acid identity,consistent with a WGD event in the lineage leading to S.coeruleus;(ii)the S.roeselii genome possesses extremely short intergenic regions,implying that the lengths of intergenic regions are under strong selection;(iii)the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs;(iv)gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa,possibly relating to the remarkable regenerative ability in Stentor.This study offers new insights into the evolutionary dynamics of ciliate genomes,with implications for understanding of the processes underlying the evolution of genomic complexity.
基金supported by the Sichuan Science and Technology Program(grant number 2024NSFSC1518 to G.H.)the National Natural Science Foundation of China(grant number 82402203 to G.H.)+3 种基金the 1.3.5 Project for Disciplines of Excellence,West China Hospital,Sichuan University(grant number ZYJC20002 to H.Y.)the Major Project of the National Social Science Foundation of China(grant number 23&ZD203 to G.H.)the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(grant numbers 2022FGKFKT05 to G.H.and 2024FGKFKT02 to M.W.)the Center for Archaeological Science of Sichuan University(grant numbers 23SASA01 and 24SASB03 to G.H.).
文摘Rapid advances in sequencing and bioinformatics have profoundly enhanced disease understanding[1],while integrated genomic analyses reveal regulatory networks governing biological processes[2].However,research remains disproportionately focused on populations of European ancestry or other groups with large sample sizes,such as Han Chinese,leaving many ethnically diverse and underrepresented populations disadvantaged in genomic medicine[3].Complex human demographic processes influence allele frequencies,define gene sets under selective constraints,and inform variant-filtering strategies crucial for genetic disease diagnosis and genetic counseling.This imbalance limits the global applicability of genomic findings and exacerbates existing health disparities.By prioritizing high-quality genome sequencing from underrepresented populations,researchers can uncover novel genetic variants,refine disease risk predictions,and promote equitable access to precision medicine.
基金supported by the National Natural Science Foundation of China (32322059 and 32272124)China Postdoctoral Science Foundation (2023M733807)+2 种基金Frontiers Science Center for Molecular Design Breeding (2022TC152)Pinduoduo-China Agricultural University Research Fund (PC2023B01016)the 2115 Talent Development Program of China Agricultural University.
文摘Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.
基金supported by the National Key R&D Program of China(Grant Nos.2022YFC3400300 and 2023YFF0613300)the National Natural Science Foundation of China(Grant Nos.32200510,32400509,32125009,32070663,32371516,and 32400520).
文摘Recent developments in PacBio high-fidelity(HiFi)sequencing technologies have transformed genomic research,with circular consensus se-quencing now achieving 99.9%accuracy for long(up to 25 kb)single-molecule reads.This method circumvents biases intrinsic to amplification-based approaches,enabling thorough analysis of complex genomic regions including tandem repeats,segmental duplications,ribosomal DNA(rDNA)arrays,and centromeresl as well as direct detection of base modifications,furnishing both sequence and epigenetic data concurrently.This has streamlined a number of tasks including genome assembly,variant detection,and full-length transcript analysis.This review provides a comprehensive overview of the applications and challenges of HiFi sequencing across various fields,including genomics,transcriptomics,and epigenetics.By delineating the evolving landscape of HiFi sequencing in multi-omics research,we highlight its potential to deepen our under-standingofgeneticmechanisms and to advance precision medicine.
文摘The rapid advancement of nanopore metagenomic sequencing has revolutionized microbiome research,enabling significant breakthroughs in the study of microbial communities,ecological dynamics,and genome-level functions[1–5].This innovative sequencing technology stands out due to its ability to generate long sequencing reads,which are pivotal in resolving complex microbial genomic structures that short-read sequencing often fails to address[2,6].
文摘Diversity array technology （DART^TM） was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice （Oryza sativa L.）genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc （Numerical taxonomy system for cluster and ordination analysis, v. 2.02j） software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple sequence repeats genotyping outline and varieties＇ pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.
