ArticleBMC genomics2011
Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 75 citations in OpenAlex.
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- Discovery of prolactin-like in lamprey: Role in osmoregulation and new insight into the evolution of the growth hormone/prolactin family.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Whole-Genome Duplications and the Diversification of the Globin-X Genes of Vertebrates.Genome biology and evolution · 2021Article
- Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution.Nature communications · 2021Article
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- Origin and evolution of the Rax homeobox gene by comprehensive evolutionary analysis.FEBS open bio · 2020Article
- Divergent genes encoding the putative receptors for growth hormone and prolactin in sea lamprey display distinct patterns of expression.Scientific reports · 2020Article
- Corticotropin-Releasing Hormone (CRH) Gene Family Duplications in Lampreys Correlate With Two Early Vertebrate Genome Doublings.Frontiers in neuroscience · 2020Article
- Lampreys, the jawless vertebrates, contain three Pax6 genes with distinct expression in eye, brain and pancreas.Scientific reports · 2019Article
- An atlas of anterior hox gene expression in the embryonic sea lamprey head: Hox-code evolution in vertebrates.Developmental biology · 2019Article
- Duplicated Myosin V Genes in Teleosts Show Evolutionary Rate Variations among the Motor and Cargo-Binding Domains.Genome biology and evolution · 2019Article
- Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.Briefings in functional genomics · 2018Review
- The Reprimo Gene Family: A Novel Gene Lineage in Gastric Cancer with Tumor Suppressive Properties.International journal of molecular sciences · 2018Review
- The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.Nature genetics · 2018Article
- Voltage-gated sodium channel gene repertoire of lampreys: gene duplications, tissue-specific expression and discovery of a long-lost gene.Proceedings. Biological sciences · 2017Article
- Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Early Evolution of Vertebrate Mybs: An Integrative Perspective Combining Synteny, Phylogenetic, and Gene Expression Analyses.Genome biology and evolution · 2015Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.
resultsSeven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.
conclusionsOur results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.
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