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Computational methods for the identification of genes in vertebrate genomic sequences

J. Claverie
1997 Human Molecular Genetics  
Research into new methods to identify genes in anonymous genomic sequences has been going on for more than 15 years.  ...  organization of multi-exon vertebrate genes.  ...  The difficulty of accurately predicting the location of vertebrate promoters has been well documented in recent reviews (2, (85) (86) (87) .  ... 
doi:10.1093/hmg/6.10.1735 pmid:9300666 fatcat:qwjro6ogvnftfd4g67kskvxxie

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

W. Iwasaki, T. Fukunaga, R. Isagozawa, K. Yamada, Y. Maeda, T. P. Satoh, T. Sado, K. Mabuchi, H. Takeshima, M. Miya, M. Nishida
2013 Molecular biology and evolution  
Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies  ...  A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating  ...  This work was supported by the Japan Society for the Promotion of Science (Grant Numbers 13556028, 19207007, 23370041, 23710231, 178087, 248046, and 258048) and the Japan Science and Technology Agency  ... 
doi:10.1093/molbev/mst141 pmid:23955518 pmcid:PMC3808866 fatcat:k2557e54xzhgblrayc3vkt2w5m

Evolutionary history of the reprimo tumor suppressor gene family in vertebrates with a description of a new reprimo gene lineage

Ignacio A. Wichmann, Kattina Zavala, Federico G. Hoffmann, Michael W. Vandewege, Alejandro H. Corvalán, Julio D. Amigo, Gareth I. Owen, Juan C. Opazo
2016 Gene  
Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest.  ...  We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor  ...  In vertebrates the three members of the family (p53, p63 and p73) have been identified (Lane et al., 2011) , suggesting that the vertebrate specific whole genome duplications played a pivotal role in  ... 
doi:10.1016/j.gene.2016.07.036 pmid:27432065 fatcat:uozn2tohrfe25ofn67g34croim

Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution

Jun Inoue, Noriyuki Satoh
2018 Molecular biology and evolution  
genes should also be considered in future studies of the origin of paraxial muscle.  ...  As orthologs of most paraxial muscle genes were present in ambulacrarians, in addition to expression patterns of related genes and functions of the two protein isoforms, regulatory mechanisms of muscle  ...  This work was supported by the Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research (B) (16H04824) to N.S. and (C) (15K07172) to J.I.  ... 
doi:10.1093/molbev/msy002 pmid:29319812 pmcid:PMC5888912 fatcat:cn3v73bygjdsrlnvu3ha5k337u

Expression patterns of kiss2 and gpr54‐2 in Monopterus albus suggest these genes may play a role in sex reversal in fish

Ti‐Lin Yi, Meng‐Ting Pei, Dai‐Qin Yang
2019 FEBS Open Bio  
We identified only two genes: kiss2 and gpr54-2. kiss2 expression was extremely high in the gonads of males, intermediate in females, and low in intersex; and reduced in all tissues of intersex. gpr54  ...  Our objectives were to identify all kiss/gpr54 genes in the genome of M. albus and to assess their involvement in sex reversal via their expression patterns (qPCR) in females, males, and intersex specimens  ...  Acknowledgements We would like to thank the two anonymous reviewers for investing time and expertise into reviewing our manuscript.  ... 
doi:10.1002/2211-5463.12727 pmid:31446680 pmcid:PMC6768111 fatcat:p2ztjnsudre6lfftbtzkolmwaa

The animal in the genome: comparative genomics and evolution

Richard R Copley
2008 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Deus ex machina: A power, event, person, or thing that comes in the nick of time to solve a difficulty; providential interposition. Oxford English Dictionary  ...  An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components.  ...  This may be as much a sign of difficulties in reliably assigning gene orthology on a large scale, as a real indication of the extents of the conserved cores.  ... 
doi:10.1098/rstb.2007.2235 pmid:18192189 pmcid:PMC2614226 fatcat:3itk5xuprnezlbd74m7ihrqssm

The animal in the genome: comparative genomics and evolution [chapter]

Richard R. Copley
2009 Animal Evolution  
Deus ex machina: A power, event, person, or thing that comes in the nick of time to solve a difficulty; providential interposition. Oxford English Dictionary  ...  An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components.  ...  This may be as much a sign of difficulties in reliably assigning gene orthology on a large scale, as a real indication of the extents of the conserved cores.  ... 
doi:10.1093/acprof:oso/9780199549429.003.0014 fatcat:2ad6psmydrgi7fhfkevl5wijhi

Conservation and losses of avian non-coding RNA loci [article]

Paul P. Gardner, Mario Fasold, Sarah W. Burge, Maria Ninova, Jana Hertel, Stephanie Kehr, Tammy E. Steeves, Sam Griffiths-Jones, Peter F. Stadler
2014 arXiv   pre-print
These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.  ...  Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes.  ...  We thank the anonymous referees for providing invaluable suggestions that improved this work.  ... 
arXiv:1406.7140v1 fatcat:wtgnepxjsnadtkuqrzf3vfz7ru

Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebrates

Sandra Santos, Sylvie Mazan, Byrappa Venkatesh, Joëlle Cohen-Tannoudji, Bruno Quérat
2011 BMC Evolutionary Biology  
A number of genes were identified in the amphioxus genome that helped in reconstructing the ancestral environment of gpa2 and gpb5 and in describing the evolution of this environment in vertebrates.  ...  A number of genes were identified in the amphioxus genome that helped in reconstructing the ancestral environment of gpa2 and gpb5 and in describing the evolution of this environment in vertebrates.  ...  A special thank to an anonymous reviewer for the constructive comments and suggestions that greatly helped in improving the quality of this manuscript.  ... 
doi:10.1186/1471-2148-11-332 pmid:22085792 pmcid:PMC3280201 fatcat:nttujku2djh2zjinxsm7sj5vvq

Discovery of regulatory elements in vertebrates through comparative genomics

Amol Prakash, Martin Tompa
2005 Nature Biotechnology  
last column shows the GO category for which the enrichment was observed,along with the number of genes, P value, and E value of the enrichment in parentheses.  ...  The third column shows the number of genes of the cluster having any GO biological process annotation.  ...  This material is based upon work supported in part by the National Science Foundation under grant DBI-0218798 and by the National Institutes of Health under grant R01 HG02602.  ... 
doi:10.1038/nbt1140 pmid:16211068 fatcat:ukxthkobqbdypplnd4j5lgwini

Phylogenetic analysis of the Wnt gene family and discovery of an arthropod Wnt10 orthologue

E.L. Jockusch, K.A. Ober
2000 Journal of Experimental Zoology  
We have identified a novel Wnt gene in a diversity of arthropods that it is likely an orthologue of the vertebrate Wnt-10 group.  ...  Despite difficulties in assessing orthologies, all of our trees suggest that the most recent common ancestor of protostomes and deuterostomes possessed more than the five Wnt genes known from either arthropods  ...  Moulton for the blackfly data and L. Nagy for the Triops data. L. Nagy and two anonymous reviewers provided helpful comments on a draft of this paper.  ... 
doi:10.1002/1097-010x(20000815)288:2<105::aid-jez3>3.3.co;2-# pmid:10931495 fatcat:h4g7q37jlfewxa3k7kxahtprqe

Phylogenetic analysis of theWnt gene family and discovery of an arthropodWnt-10 orthologue

E.L. Jockusch, K.A. Ober
2000 Journal of Experimental Zoology  
We have identified a novel Wnt gene in a diversity of arthropods that it is likely an orthologue of the vertebrate Wnt-10 group.  ...  Despite difficulties in assessing orthologies, all of our trees suggest that the most recent common ancestor of protostomes and deuterostomes possessed more than the five Wnt genes known from either arthropods  ...  Moulton for the blackfly data and L. Nagy for the Triops data. L. Nagy and two anonymous reviewers provided helpful comments on a draft of this paper.  ... 
doi:10.1002/1097-010x(20000815)288:2<105::aid-jez3>3.0.co;2-8 pmid:10931495 fatcat:bdwgpcglqnasvh5o5lnsmzjuyy

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

Federico G. Hoffmann, Juan C. Opazo
2010 Journal of Molecular Evolution  
Subsequent rounds of tandem gene duplication and divergence originated the set of paralogs found on a given cluster in extant vertebrates.  ...  Our study supports the hypothesis that differentiation of the RLN and INSL genes took place independently in each RLN/INSL cluster after the two WGDs during the evolutionary history of vertebrates.  ...  Oliver Pearson Award from the American Society of Mammalogists (ASM).  ... 
doi:10.1007/s00239-010-9403-6 pmid:21082170 fatcat:xrahjfst5jafvct6twgbqahbzy

Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters

Görel Sundström, Tomas A Larsson, Dan Larhammar
2008 BMC Evolutionary Biology  
Ever since the theory about two rounds of genome duplication (2R) in the vertebrate lineage was proposed, the Hox gene clusters have served as the prime example of quadruplicate paralogy in mammalian genomes  ...  In teleost fishes, the observation of additional Hox clusters absent in other vertebrate lineages suggested a third tetraploidization (3R).  ...  This work was supported by grants from the Swedish Research Council and Carl Trygger's Foundation. The authors would like to thank the anonymous reviewers for comments improving the manuscript.  ... 
doi:10.1186/1471-2148-8-254 pmid:18803835 pmcid:PMC2566581 fatcat:yepxd73d2rgenkebakr4wdlkcu

Evolution of two Rh blood group-related genes of the amphioxus species Branchiostoma floridae

Takashi Kitano, Masahiro Satou, Naruya Saitou
2010 Genes & Genetic Systems  
It is likely that the four Rh family genes in vertebrates emerged by gene duplications in the common ancestor of vertebrates, and functional differentiation has occurred after the first gene duplication  ...  The corresponding regions of Rh genes from exons 2 to 7 were relatively conserved among the chordate species examined in this study.  ...  Three other genes that are homologous to Rh blood group genes have been identified in the human genome.  ... 
doi:10.1266/ggs.85.121 pmid:20558898 fatcat:nmj6tufbpbfitblgecxbhfabfy
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