GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.
Yi Shao,C. T. Chen,Hao Shen,Bin Z. He,Daqi Yu,Shuai Jiang,Shilei Zhao,Zhiqiang Gao,Zhenglin Zhu,Xi Chen,Yan Fu,Hua Chen,Hua Chen,Ge Gao,Manyuan Long,Yong Zhang +15 more
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TLDR
GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes, revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family–based methods are useful for ancient genes.Abstract:
The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family-based methods are useful for ancient genes. For SBP-dated primate-specific protein-coding genes (PSGs), we performed manual evaluation based on published PSG lists and showed that SBP generated a conservative data set of PSGs by masking less reliable syntenic regions. After assessing the coding potential based on evolutionary constraint and peptide evidence from proteomic data, we curated a list of 254 PSGs with different levels of protein evidence. This list also includes 41 candidate misannotated pseudogenes that encode primate-specific short proteins. Coexpression analysis showed that PSGs are preferentially recruited into organs with rapidly evolving pathways such as spermatogenesis, immune response, mother-fetus interaction, and brain development. For brain development, primate-specific KRAB zinc-finger proteins (KZNFs) are specifically up-regulated in the mid-fetal stage, which may have contributed to the evolution of this critical stage. Altogether, hundreds of PSGs are either recruited to processes under strong selection pressure or to processes supporting an evolving novel organ.read more
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Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly
Hongjie Li,Jasper Janssens,Maxime de Waegeneer,Sai Saroja Kolluru,Kristofer Davie,Vincent Gardeux,Wouter Saelens,Fabrice P. A. David,Maria Brbic,Katina I. Spanier,Jure Leskovec,Colleen N. McLaughlin,Qijing Xie,Robert C. Jones,Katja Brueckner,Jiwon Shim,Sudhir Gopal Tattikota,Frank Schnorrer,Katja Rust,Todd G. Nystul,Zita Carvalho-Santos,Carlos Ribeiro,Soumitra Pal,Sharvani Mahadevaraju,Teresa M. Przytycka,Aaron M. Allen,Stephen F. Goodwin,Cameron Wynn Berry,Margaret T. Fuller,Helen White-Cooper,Erika Matunis,Stephen DiNardo,Anthony Galenza,Lucy Erin O'Brien,Julian A. T. Dow,Heinrich Jasper,Brian Oliver,Norbert Perrimon,Bart Deplancke,Stephen R. Quake,Liqun Luo,Stein Aerts,Devika Agarwal,Yasir H. Ahmed-Braimah,Michelle N. Arbeitman,Majd M. Ariss,Jordan Augsburger,K. R. Ayush,Catherine C. Baker,Torsten U. Banisch,Katja Birker,Rolf Bodmer,Benjamin Bolival,Susanna E. Brantley,Julie A. Brill,Nora C Brown,Norene A. Buehner,Xiao Cai,Rita Cardoso-Figueiredo,Fernando Casares,Amy K. Chang,Thomas R. Clandinin,Sheela Crasta,Claude Desplan,Angela M. Detweiler,Darshan B. Dhakan,Erika Donà,Steffi Engert,Swann Floc'hlay,Nancy F. George,Amanda J. González-Segarra,Andrew K. Groves,Samantha C. Gumbin,Yanmeng Guo,Devon E Harris,Yael Heifetz,Stephen L. Holtz,Felix Horns,Bruno Hudry,Ruei-Jiun Hung,Yuh Nung Jan,Jacob S Jaszczak,Gregory S.X.E. Jefferis,Jim Karkanias,Timothy L. Karr,Nadja Sandra Katheder,James N. Kezos,Anna Kim,Seung K. Kim,Lutz Kockel,Nikolaos Konstantinides,Thomas B. Kornberg,Henry M. Krause,Andrew T. Labott,Meghan Laturney,Ruth Lehmann,Sarah G Leinwand,Jiefu Li,Joshua Shing Shun Li,Kai Li,Kexin Li,Liying Li,Tun Li,Maria Litovchenko,Hanji Liu,Yifang Liu,Tzu-Chiao Lu,Jonathan Ryan Manning,A. De Mase,Mikaela Matera-Vatnick,Neuza Reis Matias,Caitlin E. McDonough-Goldstein,Aaron McGeever,Alex D McLachlan,Paola Moreno-Román,Norma F. Neff,Megan Neville,Sang Ngo,Tanja Nielsen,Caitlin E. O’Brien,David Osumi-Sutherland,Mehmet Neset Özel,Irene Papatheodorou,Maja Petkovic,Ch. Pilgrim,Angela Oliveira Pisco,Carolina E. Reisenman,Erin Sanders,Gilberto dos Santos,Kristin Scott,Aparna Sherlekar,Philip Shiu,David Sims,Rene Sit,Maija Slaidina,Harold E. Smith,Gabriella R Sterne,Yu-han Su,Daniel Alexander Sutton,Marco Tamayo,Michelle Tan,Ibrahim Tastekin,Christoph Daniel Treiber,David Vacek,Georg Vogler,Scott Waddell,Wanpeng Wang,Rachel Wilson,Mariana F. Wolfner,Yiu-Cheung E. Wong,Anthony Xie,Jun Xu,Shinya Yamamoto,Jiamei Yan,Zepeng Yao,Kazuki Yoda,Ruijun Zhu,Robert P. Zinzen +157 more
TL;DR: A single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types is presented, providing an in-depth analysis of cell type–related gene signatures and transcription factor markers, as as sexual dimorphism, across the whole animal.
Journal ArticleDOI
Transcriptome and translatome co-evolution in mammals
Zhong-Yi Wang,Evgeny Leushkin,Angélica Liechti,Svetlana Ovchinnikova,Katharina Mößinger,Thoomke Brüning,Coralie Rummel,Frank Grützner,Margarida Cardoso-Moreira,Peggy Janich,David Gatfield,Boubou Diagouraga,Boubou Diagouraga,Bernard de Massy,Mark E. Gill,Antoine H.F.M. Peters,Antoine H.F.M. Peters,Simon Anders,Henrik Kaessmann +18 more
TL;DR: The authors' within-species analyses reveal that translational regulation is widespread in the different organs, in particular across the spermatogenic cell types of the testis, and provides a resource for understanding their interplay in mammalian organs.
Posted ContentDOI
Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly
Hongjie Li,Hongjie Li,Janssens J,M. De Waegeneer,Sai Saroja Kolluru,Kristofer Davie,Gardeux,Wouter Saelens,Fabrice P. A. David,Maria Brbic,Jure Leskovec,Colleen N McLaughlin,Qijing Xie,Robert C. Jones,K Brueckner,Jiwon Shim,Sudhir Gopal Tattikota,Frank Schnorrer,K Rust,K Rust,Todd G. Nystul,Zita Carvalho-Santos,Carlos Ribeiro,Soumitra Pal,Teresa M. Przytycka,Aaron M. Allen,Stephen F. Goodwin,Cameron Wynn Berry,Margaret T. Fuller,Helen White-Cooper,Erika Matunis,Stephen DiNardo,A Galenza,Lucy Erin O'Brien,Julian A. T. Dow,Heinrich Jasper,Brian Oliver,Norbert Perrimon,Bart Deplancke,Quake S,Liqun Luo,Stein Aerts +41 more
TL;DR: Tabula Drosophilae as mentioned in this paper is a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body.
Journal ArticleDOI
Developmental Gene Expression Differences between Humans and Mammalian Models
Margarida Cardoso-Moreira,Ioannis Sarropoulos,Britta Velten,Matthew Mort,David Neil Cooper,Wolfgang Huber,Henrik Kaessmann +6 more
TL;DR: A transcriptomic resource covering the development of seven organs is used to characterize the temporal profiles of human genes associated with distinct disease classes and to determine, for each human gene, the similarity of its spatiotemporal expression with its orthologs in rhesus macaque, mouse, rat, and rabbit.
Journal ArticleDOI
Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling.
Lin Liu,Lin Liu,Guangyu Wang,Liguo Wang,Chunlei Yu,Chunlei Yu,Mengwei Li,Mengwei Li,Shuhui Song,Shuhui Song,Lili Hao,Lili Hao,Lina Ma,Lina Ma,Zhang Zhang,Zhang Zhang +15 more
TL;DR: It is revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma and in combination with MGMT is effective to predict survival outcomes in a more precise manner.
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