As one of the key technologies in biomedical research,DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years.Thi...As one of the key technologies in biomedical research,DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years.This is largely due to the advent of newer generations of sequencing platforms,offering ever-faster and cheaper ways to analyze sequences.In our previous review,we looked into technical characteristics of the nextgeneration sequencers and provided prospective insights into their future development.In this article,we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.展开更多
Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-...Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.展开更多
Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent mode...Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent model system for transposon study since its genome (- 160 Mb) has been sequenced and is composed of - 65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.展开更多
基金This work was supported by the Chinese Academy of Sciences Scientific Research Equipments(Grant No.YZ200823)the Institutional Director’s Initiative Fund awarded to Jun Yu.
文摘As one of the key technologies in biomedical research,DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years.This is largely due to the advent of newer generations of sequencing platforms,offering ever-faster and cheaper ways to analyze sequences.In our previous review,we looked into technical characteristics of the nextgeneration sequencers and provided prospective insights into their future development.In this article,we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.
基金supported by the Chengdu Giant Panda Breeding Research Foundation,China(Grant No.CPF-2012-13)the Self-supporting Project of Chengdu Giant Panda Breeding Research Base,China(Grant No.2020CPBB20)+2 种基金the Sichuan International Science and Technology Innovation Cooperation/Hong Kong,Macao,and Taiwan Science and Technology Innovation Cooperation Project,China(Grant No.2019YFH0065)the National Natural Science Foundation of China(Grant No.31801048)the Highlevel Scientific Research Foundation for the Introduction of Talents of Sichuan Agricultural University of China(Grant No.03120322).
文摘Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
基金supported by grants from the National Basic Research Program(973 Program)(Nos.2006CB910401, 2006CB910403 and 2006CB910404) awarded to JY and HSthe Chinese Ministry of Science and Technology,the National Science and Technology Key Project(No. 2008ZX10004-013) awarded to JY
文摘Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution. Trichomonas vaginalis is an excellent model system for transposon study since its genome (- 160 Mb) has been sequenced and is composed of - 65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.