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The first Chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in Iguanian lizards.

Bar-Yaacov D, Bouskila A, Mishmar D - Genome Biol Evol (2013)

Bottom Line: Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups.We aimed to examine whether the same pattern of divergence could be found in nuclear genes.Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.

ABSTRACT
Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

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Pie chart summary of biological processes in the Chamaeleo chamaeleone transcriptome. The chart was assembled using Blast2GO. Notably, certain contigs (genes) could be listed in multiple processes.
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evt131-F1: Pie chart summary of biological processes in the Chamaeleo chamaeleone transcriptome. The chart was assembled using Blast2GO. Notably, certain contigs (genes) could be listed in multiple processes.

Mentions: The assembled contigs were annotated using Blast2GO (Conesa et al. 2005) (fig. 1). Specifically, our transcriptome sequences were screened using BlastX against the NCBI NR database. A “HIT” for a contig was listed only if it had a value greater than 1.0E−6. The best hits were ranked according to Blast2GO default parameters. Mapping and annotation steps were performed using the Blast2GO default parameters. Supplementary table S1, Supplementary Material online, summarizes all the assembled contigs and Blast hits which are available online (http://lifeserv.bgu.ac.il/wb/dmishmar/pages/supplementary-files.php, last accessed September 18, 2013). Blast2GO was used to construct a biological process graph using 36,740 human annotated transcripts.


The first Chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in Iguanian lizards.

Bar-Yaacov D, Bouskila A, Mishmar D - Genome Biol Evol (2013)

Pie chart summary of biological processes in the Chamaeleo chamaeleone transcriptome. The chart was assembled using Blast2GO. Notably, certain contigs (genes) could be listed in multiple processes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814190&req=5

evt131-F1: Pie chart summary of biological processes in the Chamaeleo chamaeleone transcriptome. The chart was assembled using Blast2GO. Notably, certain contigs (genes) could be listed in multiple processes.
Mentions: The assembled contigs were annotated using Blast2GO (Conesa et al. 2005) (fig. 1). Specifically, our transcriptome sequences were screened using BlastX against the NCBI NR database. A “HIT” for a contig was listed only if it had a value greater than 1.0E−6. The best hits were ranked according to Blast2GO default parameters. Mapping and annotation steps were performed using the Blast2GO default parameters. Supplementary table S1, Supplementary Material online, summarizes all the assembled contigs and Blast hits which are available online (http://lifeserv.bgu.ac.il/wb/dmishmar/pages/supplementary-files.php, last accessed September 18, 2013). Blast2GO was used to construct a biological process graph using 36,740 human annotated transcripts.

Bottom Line: Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups.We aimed to examine whether the same pattern of divergence could be found in nuclear genes.Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.

ABSTRACT
Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

Show MeSH
Related in: MedlinePlus