第27届国际动植物基因组学大会要事记
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摘要
基因组学是对所有基因进行基因组作图(包括遗传图谱、物理图谱、转录本图谱)、核苷酸序列分析、基因定位和基因功能分析的一门科学。为探索中外基因组学研究的前沿问题,总结了第27届动植物基因组国际会议上展示的15个相关主题的主要成就,代表目前模式生物、作物、水生生物和微生物基因组学的研究热点。基因组学不仅涉及生物领域,还涉及与其他学科的交叉融合,如医学、环境学、生物学等,基因组学的进步不断推动新技术、新领域如三维基因组学和生态基因组学的产生。此外,简要回顾了本届会议上呈现的新兴研究手段为基因组学研究带来的革命性进展,并对未来的研究方向进行了展望。
Genomics is defined as the science of mapping the genome of all genes(including genetic, physical and transcriptional maps), nucleotide sequence analyses, gene localization and function analyses. In order to explore the global frontiers of genomics research,this paper summarized the major achievements of 15 related research topics in the plant and animal genome ⅩⅩⅦ conference, representing the current genomics research hotspots of model organisms, crops, aquatic organisms and microorganisms. Genomics involved not only the biological field, but also the integration with other disciplines, such as medicine, environmental and biological sciences, etc. The progresses in genomics constantly promoted the emergence of new technologies and new fields, such as three dimensional genomics, and ecological genomics. The revolutionary advances by the emerging research methods in genomics research were briefly reviewed, and the research perspectives were summarized in the paper.
Genomics is defined as the science of mapping the genome of all genes(including genetic, physical and transcriptional maps), nucleotide sequence analyses, gene localization and function analyses. In order to explore the global frontiers of genomics research,this paper summarized the major achievements of 15 related research topics in the plant and animal genome ⅩⅩⅦ conference, representing the current genomics research hotspots of model organisms, crops, aquatic organisms and microorganisms. Genomics involved not only the biological field, but also the integration with other disciplines, such as medicine, environmental and biological sciences, etc. The progresses in genomics constantly promoted the emergence of new technologies and new fields, such as three dimensional genomics, and ecological genomics. The revolutionary advances by the emerging research methods in genomics research were briefly reviewed, and the research perspectives were summarized in the paper.
引文
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[14] TETTELIN H,MASIGNANI V,CIESLEWICZ M J,et al.Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:implications for the microbial “pan-genome” [J].Proceedings of the National Academy of Sciences of the United States of America,2005,102(39):13950-13955.
[15] ZHAO Q,FENG Q,LU H,et al.Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice [J].Nature Genetics,2018,50(2):278-284.
[16] MONTENEGRO J D,GOLICZ A A,BAYER P E,et al.The pangenome of hexaploid bread wheat [J].Plant Journal,2017,90(5):1007-1013.
[17] SUZUKI M M,BIRD A.DNA methylation landscapes:provocative insights from epigenomics [J].Nature Reviews Genetics,2008,9(6):465-476.
[18] DENG X,SONG X W,WEI L Y,et al.Epigenetic regulation and epigenomic landscape in rice [J].National Science Review,2016,3(3):309-327.
[19] BARTON N H.What role does natural selection play in speciation?[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2010,365(1547):1825-1840.
[20] EVANS L M,SLAVOV G T,RODGERS-MELNICK E,et al.Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations [J].Nature Genetics,2014,46(10):1089-1096.
[21] ABROUK M,MURAT F,PONT C,et al.Paleogenomics of plants:synteny-based modelling of extinct ancestors [J].Trends in Plant Science,2010,15(9):479-487.
[22] WANG J P,YU J X,SUN P C,et al.Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses [J].Frontiers in Genetics,2016,7(1):174.
[23] MING R,VANBUREN R,WAI C M,et al.The pineapple genome and the evolution of CAM photosynthesis [J].Nature Genetics,2015,47(12):1435-1442.
[24] GARAN S A,FREITAG W,YAGHMAIE F,et al.Phenomics:a new direction for the study of neuroendocrine aging [J].Experimental Gerontology,2003,38(1/2):218.
[25] DRECCER M F,MOLERO G,RIVERA-AMADO C,et al.Yielding to the image:how phenotyping reproductive growth can assist crop improvement and production [J].Plant Science,2019,282(1):73-82.
[26] LEI L,POETS A M,LIU C,et al.Discovery of barley gene candidates for low temperature and drought tolerance via environmental association [J].bioRxiv,2018,DOI:http://dx.doi.org/10.1101/405399.
[27] SCHMID M,FREI D,PATRIGNANI A,et al.Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long,near identical repeats [J].Nucleic Acids Research,2018,46(17):8953-8965.
[28] WU Y,SUN Y,SUN S,et al.Aneuploidization under segmental allotetraploidy in rice and its phenotypic manifestation [J].Theoretical and Applied Genetics,2018,131(6):1273-1285.
[29] JAIN M,OLSEN H E,TURNER D J,et al.Linear assembly of a human centromere on the Y chromosome [J].Nature Biotechnology,2018,36(4):321-323.
[30] KENT W J,SUGNET C W,FUREY T S,et al.The human genome browser at UCSC [J].Genome Research,2002,12(6):996-1006.
[31] CHUN C S,PELUSO P,SEDLAZECK F J,et al.Phased diploid genome assembly with single-molecule real-time sequencing [J].Nature Methods,2016,13(12):1050-1054.
[32] WUYUN T N,WANG L,LIU H M,et al.The hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesis [J].Molecular Plant,2018,11(3):429-442.
[33] YANG J H,LIU D Y,WANG X W,et al.The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeology gene expression influencing selection [J].Nature Genetics,2016,48(10):1225-1232.
[34] BADOUIN H,GOUZY J,GRASSA C J,et al.The sunflower genome provides insights into oil metabolism,flowering and Asterid evolution [J].Nature,2017,546(7656):148-152.
[35] LIU Q,LI X Y,ZHOU X Y,et al.The DNA landscape in Avena:chromosome and genome evolution defined by major repetitive DNA classes in whole-genome sequence reads [J].BMC Plant Biology,2019,19(1):226.
[36] YIN D M,JI C M,MA X L,et al.Genome of an allotetraploid wild peanut Arachis monticola:a de novo assembly [J].GigaScience,2018,7(6):giy066.
[37] ANNUNZIATO A.DNA packaging:nucleosomes and chromatin [J].Nature Education,2008,1(1):26.
[2] HUANG X H,ZHAO Y,WEI X H,et al.Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm [J].Nature Genetics,2012,44(3):32-39.
[3] HUANG X H,YANG S H,GONG J Y,et al.Genomic architecture of heterosis for yield traits in rice [J].Nature,2016,537(7622):629-633.
[4] BOYLE E A,LI Y I,PRITCHARD J K.An expanded view of complex traits:from polygenic to omnigenic [J].Cell,2018,169(7):1177-1186.
[5] RAYMOND O,GOUZY J,JUST J,et al.The Rosa genome provides new insights into the domestication of modern roses [J].Nature Genetics,2018,50(6):772-777.
[6] OJEDA D L,MATTILA T,RUTTINK T,et al.Utilization of tissue ploidy level variation in de novo transcriptome assembly of Pinus sylvestris [J].Bio Rxiv,2018,DOI:http://dx.doi.org/10.1101/495689.
[7] WANG M J,TU L L,YUAN D J,et al.Reference genome sequences of two cultivated allotetraploid cottons,Gossypium hirsutum and Gossypium barbadense [J].Nature Genetics,2019,51(2):224-229.
[8] FLEMING M B,PATTERSON E L,REEVES P A,et al.Exploring the fate of mRNA in aging seeds:protection,destruction,or slow decay?[J].Journal of Experimental Botany,2018,69(18):4309-4321.
[9] 李国亮,阮一骏,谷瑞生,等.起航三维基因组学研究 [J].科学通报,2014,59(13):1165-1172.
[10] CHRISTIN P A,BOXALL S F,GREGORY R,et al.Parallel recruitment of multiple genes into C4 photosynthesis [J].Genome Biology and Evolution,2013,5(11):2174-2187.
[11] ZOU C S,LI L T,MIKI D,et al.The genome of broomcorn millet [J].Nature Communications,2019,10(1):436.
[12] HANDELSMAN J,RONDON M R,BRADY S F,et al.Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products [J].Chemistry and Biology,1998,5(10):R245-R249.
[13] JI P F,ZHANG Y M,WANG J F,et al.MetaSort untangles metagenome assembly by reducing microbial community complexity [J].Nature Communications,2017,8(1):14306.
[14] TETTELIN H,MASIGNANI V,CIESLEWICZ M J,et al.Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:implications for the microbial “pan-genome” [J].Proceedings of the National Academy of Sciences of the United States of America,2005,102(39):13950-13955.
[15] ZHAO Q,FENG Q,LU H,et al.Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice [J].Nature Genetics,2018,50(2):278-284.
[16] MONTENEGRO J D,GOLICZ A A,BAYER P E,et al.The pangenome of hexaploid bread wheat [J].Plant Journal,2017,90(5):1007-1013.
[17] SUZUKI M M,BIRD A.DNA methylation landscapes:provocative insights from epigenomics [J].Nature Reviews Genetics,2008,9(6):465-476.
[18] DENG X,SONG X W,WEI L Y,et al.Epigenetic regulation and epigenomic landscape in rice [J].National Science Review,2016,3(3):309-327.
[19] BARTON N H.What role does natural selection play in speciation?[J].Philosophical Transactions of the Royal Society B-Biological Sciences,2010,365(1547):1825-1840.
[20] EVANS L M,SLAVOV G T,RODGERS-MELNICK E,et al.Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations [J].Nature Genetics,2014,46(10):1089-1096.
[21] ABROUK M,MURAT F,PONT C,et al.Paleogenomics of plants:synteny-based modelling of extinct ancestors [J].Trends in Plant Science,2010,15(9):479-487.
[22] WANG J P,YU J X,SUN P C,et al.Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses [J].Frontiers in Genetics,2016,7(1):174.
[23] MING R,VANBUREN R,WAI C M,et al.The pineapple genome and the evolution of CAM photosynthesis [J].Nature Genetics,2015,47(12):1435-1442.
[24] GARAN S A,FREITAG W,YAGHMAIE F,et al.Phenomics:a new direction for the study of neuroendocrine aging [J].Experimental Gerontology,2003,38(1/2):218.
[25] DRECCER M F,MOLERO G,RIVERA-AMADO C,et al.Yielding to the image:how phenotyping reproductive growth can assist crop improvement and production [J].Plant Science,2019,282(1):73-82.
[26] LEI L,POETS A M,LIU C,et al.Discovery of barley gene candidates for low temperature and drought tolerance via environmental association [J].bioRxiv,2018,DOI:http://dx.doi.org/10.1101/405399.
[27] SCHMID M,FREI D,PATRIGNANI A,et al.Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long,near identical repeats [J].Nucleic Acids Research,2018,46(17):8953-8965.
[28] WU Y,SUN Y,SUN S,et al.Aneuploidization under segmental allotetraploidy in rice and its phenotypic manifestation [J].Theoretical and Applied Genetics,2018,131(6):1273-1285.
[29] JAIN M,OLSEN H E,TURNER D J,et al.Linear assembly of a human centromere on the Y chromosome [J].Nature Biotechnology,2018,36(4):321-323.
[30] KENT W J,SUGNET C W,FUREY T S,et al.The human genome browser at UCSC [J].Genome Research,2002,12(6):996-1006.
[31] CHUN C S,PELUSO P,SEDLAZECK F J,et al.Phased diploid genome assembly with single-molecule real-time sequencing [J].Nature Methods,2016,13(12):1050-1054.
[32] WUYUN T N,WANG L,LIU H M,et al.The hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesis [J].Molecular Plant,2018,11(3):429-442.
[33] YANG J H,LIU D Y,WANG X W,et al.The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeology gene expression influencing selection [J].Nature Genetics,2016,48(10):1225-1232.
[34] BADOUIN H,GOUZY J,GRASSA C J,et al.The sunflower genome provides insights into oil metabolism,flowering and Asterid evolution [J].Nature,2017,546(7656):148-152.
[35] LIU Q,LI X Y,ZHOU X Y,et al.The DNA landscape in Avena:chromosome and genome evolution defined by major repetitive DNA classes in whole-genome sequence reads [J].BMC Plant Biology,2019,19(1):226.
[36] YIN D M,JI C M,MA X L,et al.Genome of an allotetraploid wild peanut Arachis monticola:a de novo assembly [J].GigaScience,2018,7(6):giy066.
[37] ANNUNZIATO A.DNA packaging:nucleosomes and chromatin [J].Nature Education,2008,1(1):26.