项目经验节选

合作文章发表

  1. Song N, Zhao X, Cai C and Gao T. Profile of the genomic characteristics and comparative studies of five Trichiuridae species by genome survey sequencing. Front Mar Sci. 2022;9:962307. doi: 10.3389/fmars.2022.962307
  2. Fu Y, Liu H, Dou J, et al. IAnimal: a cross-species omics knowledgebase for animals. Nucleic Acids Res. 2022;gkac936. doi:10.1093/nar/gkac936
  3. Liu L, Liu Q, Gao T. Genome-wide survey reveals the phylogenomic relationships of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes). ZooKeys. 2022;1129:55-72.
  4. Jin W, Cao XJ, Ma XY, et al. Chromosome-level genome assembly of the freshwater snail Bellamya purificata (Caenogastropoda). Zool Res. 2022;43(4):683-686. doi:10.24272/j.issn.2095-8137.2022.118
  5. Han ZQ, Gao TX, Lou FR, Liu Q. Charybdisjaponica genome provides insights into desiccation adaptation and sex-determining region. Zool Res. 2022;43(6):927-930. doi:10.24272/j.issn.2095-8137.2022.155
  6. Li J, Fu C, Ai Q, et al. Whole-genome resequencing reveals complex effects of geographical-palaeoclimatic interactions on diversification of moustache toads in East Asia. Mol Ecol. 2022;10.1111/mec.16781. doi:10.1111/mec.16781
  7. Lu M, Li Z, Zhu ZY, et al. Changes in Ploidy Drive Reproduction Transition and Genomic Diversity in a Polyploid Fish Complex. Mol Biol Evol. 2022;39(9):msac188. doi:10.1093/molbev/msac188
  8. Zhang Y, Wang X, Shi H, et al. Comparative transcriptomic analysis of the liver and spleen in marbled rockfish (Sebastiscus marmoratus) challenged with polyriboinosinic polyribocytidylic acid (poly(I:C)). Aquaculture. 2022;554:738144.
  9. Liu S, Fang S, Cong B, et al. The Antarctic Moss Pohlia nutans Genome Provides Insights Into the Evolution of Bryophytes and the Adaptation to Extreme Terrestrial Habitats. Front Plant Sci. 2022;13:920138. doi:10.3389/fpls.2022.920138
  10. Zhao L, Liu S, Wang S, Yang T, Liu Q and Gao T. Chromosomal Assembly of the Hexagrammos agrammus Genome via Third-Generation DNA Sequencing and Hi-C Technology. Front Mar Sci. 2022;9:923005. doi: 10.3389/fmars.2022.923005
  11. He W, Shi M, Xia X-Q, Zhang W, Yao W and Gao T. The chromosome-level genome assembly of goldstripe ponyfish (Karalla daura) reveals its similarity to Chinese sillago on contracted immune gene families. Front Mar Sci. 2022;9:1049138. doi: 10.3389/fmars.2022.1049138
  12. Han Z, Liu M, Liu Q, Zhai H, Xiao S, Gao T. Chromosome-level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater. Mol Ecol Resour. 2021;21(6):2022-2033. doi:10.1111/1755-0998.13382
  13. Zhao L, Xu S, Han Z, et al. Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus. Genome Biol Evol. 2021;13(2):evaa246. doi:10.1093/gbe/evaa246
  14. Fu Y, Fan P, Wang L, et al. Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data. J Anim Sci. 2021;99(2):skab018. doi:10.1093/jas/skab018
  15. Xiao SJ, Mou ZB, Yang RB, et al. Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau. Zool Res. 2021;42(4):502-513. doi:10.24272/j.issn.2095-8137.2021.096
  16. Xiao S, Mou Z, Fan D, et al. Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation. iScience. 2020;23(9):101497. doi:10.1016/j.isci.2020.101497
  17. Fu Y, Xu J, Tang Z, et al. A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model. Commun Biol. 2020;3(1):502. doi:10.1038/s42003-020-01233-4
  18. An D, Zhou Y, Li C, et al. Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela. Proc Natl Acad Sci. 2019;116(38):18893-18899. doi:10.1073/pnas.1910401116
  19. Xu S, Xiao S, Zhu S, et al. A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. Gigascience. 2018;7(9):giy108. doi:10.1093/gigascience/giy108
  20. Zhu L, Deng C, Zhao X, et al. Endangered Père David's deer genome provides insights into population recovering. Evol Appl. 2018;11(10):2040-2053. doi:10.1111/eva.12705
  21. Reyes-Chin-Wo S, Wang Z, Yang X, et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun. 2017;8:14953. doi:10.1038/ncomms14953
  22. Zhang GQ, Xu Q, Bian C, et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Sci Rep. 2016;6:19029. doi:10.1038/srep19029
  23. Bai H, Guo X, Zhang D, et al. The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. Genome Biol Evol. 2014;6(12):3122-3136. doi:10.1093/gbe/evu242
  24. Wu J, Wang Z, Shi Z, et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23(2):396-408. doi:10.1101/gr.144311.112
  25. Wang K, Wang Z, Li F, et al. The draft genome of a diploid cotton Gossypium raimondii. Nat Genet. 2012;44(10):1098-1103. doi:10.1038/ng.2371
  26. Wang Z, Hobson N, Galindo L, et al. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J. 2012;72(3):461-473. doi:10.1111/j.1365-313X.2012.05093.x
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龙舌兰亚科基因组组装


组装物种:龙舌兰(Agave hybrid NO.11648)


项目亮点:中国热带农业科学院南亚热带作物研究所剑麻研究团队在龙舌兰亚科基因组及CAM进化机制上取得进展

经典案例

 

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双线巨篷蛞蝓基因组组装注释


组装物种:双线巨篷蛞蝓(Meghimatiumbilineatum)


项目亮点:组装陆地蛞蝓物种的基因组将有助于强化本物种适应进化的研究,也为更深入研究其生态适应性进化分子机制和潜在的药用资源遗传提供理论基础。

8倍体草莓基因组组装


组装物种:栽培草莓(Fragaria x ananassa)


项目亮点:首个组装到单倍型及T2T水平的八倍体草莓基因组
 

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海星染色体基因组组装


组装物种:多棘海盘车(Asterias amurensis)


项目亮点:在海星多棘海盘车的遗传学、动力学和进化提供了有价值的基因组资源。

经典案例

 

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鲫鱼染色体水平基因组组装


组装物种:鲫鱼(Echeneis naucrates)


项目亮点:组装的鲫鱼基因组有着高度完整性、连续性和准确性。

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同源四倍体鲫候选性别决定 基因挖掘


组装物种:同源四倍体鲫(Autotetraploid
Carassius auratus)

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白果草莓基因组组装


组装物种:栽培草莓(Fragariaxananassa)


项目亮点:获得了八倍体白果栽培草莓品种“初恋”的高质量单倍型基因组。

经典案例

 

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水稻超大粒形成的分子基础 解析

 

组装物种:水稻(Oryza sativaL.)
 

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二倍体和四倍体泥鳅单倍型 基因组组装以及鱼类气呼吸 相关基因Mex3a的鉴定

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经典案例

 

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基于转分化方式改造成纤维 细胞为主动脉瓣细胞
 

项目亮点:研究证明直接转分化技术比iPSCs技术具有更低的肿瘤形成风险,因此更适合临床应用

经典案例

 

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单倍体染色体水平基因组为太平洋秋刀鱼迁徙生活方式和种群多样性的分子适应性提供了见解

 

组装物种:太平洋秋刀鱼(Cololabis saira)

 

项目亮点:成功组装了太平洋秋刀鱼染色体水平单

腐烂茎线虫染色体水平基因组解析

 

腐烂茎线虫(Dity/enchusdestructor)

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经典案例

 

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黄河濒危特有鱼类大鼻吻鮈的T2T基因组构建

项目亮点:成功构建了Rhinogobio nasutus的T2T级别高质量基因组

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ISPL10的表观遗传调控增强水稻品种的区域适应性

项目亮点:揭示了水稻抽穗日期的调控机制,有助于培育出适应不同区域的水稻品种