Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case
<p>Abstract</p> <p>Background</p> <p>In 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...
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| Format: | Article |
| Language: | English |
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BMC
2011-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/325 |
| _version_ | 1828811024778657792 |
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| author | Kuraku Shigehiro Hildebrand Falk Qiu Huan Meyer Axel |
| author_facet | Kuraku Shigehiro Hildebrand Falk Qiu Huan Meyer Axel |
| author_sort | Kuraku Shigehiro |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>In 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 (<it>KCNA</it>) family, whose members are mostly single-exon.</p> <p>Results</p> <p>Seven sea lamprey <it>KCNA </it>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 <it>KCNA </it>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.</p> <p>Conclusions</p> <p>Our 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.</p> |
| first_indexed | 2024-12-12T09:20:36Z |
| format | Article |
| id | doaj.art-74496a6ff3954f62bf141c63b82f1ede |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T09:20:36Z |
| publishDate | 2011-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-74496a6ff3954f62bf141c63b82f1ede2022-12-22T00:29:13ZengBMCBMC Genomics1471-21642011-06-0112132510.1186/1471-2164-12-325Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test caseKuraku ShigehiroHildebrand FalkQiu HuanMeyer Axel<p>Abstract</p> <p>Background</p> <p>In 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 (<it>KCNA</it>) family, whose members are mostly single-exon.</p> <p>Results</p> <p>Seven sea lamprey <it>KCNA </it>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 <it>KCNA </it>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.</p> <p>Conclusions</p> <p>Our 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.</p>http://www.biomedcentral.com/1471-2164/12/325 |
| spellingShingle | Kuraku Shigehiro Hildebrand Falk Qiu Huan Meyer Axel Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case BMC Genomics |
| title | Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case |
| title_full | Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case |
| title_fullStr | Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case |
| title_full_unstemmed | Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case |
| title_short | Unresolved orthology and peculiar coding sequence properties of lamprey genes: the <it>KCNA </it>gene family as test case |
| title_sort | unresolved orthology and peculiar coding sequence properties of lamprey genes the it kcna it gene family as test case |
| url | http://www.biomedcentral.com/1471-2164/12/325 |
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