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Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopt...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338709/ https://www.ncbi.nlm.nih.gov/pubmed/22558409 http://dx.doi.org/10.1371/journal.pone.0036256 |
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author | Chen, Ming Zou, Ming Yang, Lei He, Shunping |
author_facet | Chen, Ming Zou, Ming Yang, Lei He, Shunping |
author_sort | Chen, Ming |
collection | PubMed |
description | The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences. |
format | Online Article Text |
id | pubmed-3338709 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33387092012-05-03 Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing Chen, Ming Zou, Ming Yang, Lei He, Shunping PLoS One Research Article The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences. Public Library of Science 2012-04-27 /pmc/articles/PMC3338709/ /pubmed/22558409 http://dx.doi.org/10.1371/journal.pone.0036256 Text en Chen et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Chen, Ming Zou, Ming Yang, Lei He, Shunping Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title | Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title_full | Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title_fullStr | Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title_full_unstemmed | Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title_short | Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing |
title_sort | basal jawed vertebrate phylogenomics using transcriptomic data from solexa sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338709/ https://www.ncbi.nlm.nih.gov/pubmed/22558409 http://dx.doi.org/10.1371/journal.pone.0036256 |
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