一个ZP的大型国际研究项目从2006年起搜集样本,对数百种哺乳动物的基因组序列开展测序,并对测序结果进行解读和系统比较,从分子、种群和物种水平的变化,揭示人类和其他哺乳动物的基因组在演化过程中的发展等。本文是基因组学和进化生物学、人的演化、人类疾病等关联的基础科学研究论文。
(Translated by Baidu: )
Science's Heavyweight Special Topic: 11 Papers Published Together, Understanding the New Era of Humanity, Here Comes! Gene evolution
A large-scale international research project of ZP has been collecting samples since 2006, sequencing the genome sequences of hundreds of mammals, interpreting and systematically comparing the sequencing results, revealing the evolution of human and other mammalian genomes through changes at the molecular, population, and species levels. This paper is a basic scientific research paper related to genomics, evolutionary biology, human evolution, human diseases, etc.
(百度翻訳: )
『科学』重要ポイント:11本の論文が一斉に発表され、人類の新時代を理解し、来た!遺伝子進化
1つのZPの大型国際研究プロジェクトは2006年からサンプルを収集し、数百種類の哺乳動物のゲノム配列に対して配列決定を展開し、配列決定結果に対して解読と系統比較を行い、分子、個体群と種レベルの変化から、人類と他の哺乳動物の遺伝子群の進化過程における発展などを明らかにした。本文はゲノム学と進化生物学、人の進化、人間疾患などの関連基礎科学研究論文である。
学术经纬
2023/05/04
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论文五
论文六
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论文标题:Integrating gene annotation with orthology inference at scale
作者:Bogdan M. Kirilenko, Chetan Munegowda, Ekaterina Osipova, David Jebb, Virag Sharma, Moritz Blumer, Ariadna E. Morales, Alexis-Walid Ahmed, Dimitrios-Georgios Kontopoulos, Leon Hilgers, Kerstin Lindblad-Toh, Elinor K. Karlsson, Zoonomia Consortium‡, Michael Hiller, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Bruce W. Birren, Kevin R. Bredemeyer, Ana M. Breit, Matthew J. Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X. Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M. Foley, Karin Forsberg-Nilsson, Carlos J. Garcia, John Gatesy, Steven Gazal, Diane P. Genereux, Linda Goodman, Jenna Grimshaw, Michaela K. Halsey, Andrew J. Harris, Glenn Hickey, Michael Hiller, Allyson G. Hindle, Robert M. Hubley, Graham M. Hughes, Jeremy Johnson, David Juan, Irene M. Kaplow, Elinor K. Karlsson, Kathleen C. Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M. Korstian, Amanda Kowalczyk, Sergey V. Kozyrev, Alyssa J. Lawler, Colleen Lawless, Thomas Lehmann, Danielle L. Levesque, Harris A. Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D. Marinescu, Tomas Marques-Bonet, Victor C. Mason, Jennifer R. S. Meadows, Wynn K. Meyer, Jill E. Moore, Lucas R. Moreira, Diana D. Moreno-Santillan, Kathleen M. Morrill, Gerard Muntané, William J. Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S. Paulat, Andreas R. Pfenning, BaDoi N. Phan, Katherine S. Pollard, Henry E. Pratt, David A. Ray, Steven K. Reilly, Jeb R. Rosen, Irina Ruf, Louise Ryan, Oliver A. Ryder, Pardis C. Sabeti, Daniel E. Schäffer, Aitor Serres, Beth Shapiro, Arian F. A. Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M. Storer, Kevin A. M. Sullivan, Patrick F. Sullivan, Elisabeth Sundström, Megan A. Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Xiaomeng Zhang
期刊:Science
发表时间:2023/04/28
数字识别码:10.1126/science.abn3107
摘要:Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.
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