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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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Schematic phylogenetic tree demonstrating the presence or absence of COX8 across the vertebrate phylogeny. Letters above each branch indicate the presence of the relevant COX8 isoforms. Non: total absence of all COX8 isoforms. Notably, the suborders Iguania and Serpentes are labeled. The topology of the tree is adopted from NCBI Taxonomy (see URL in Material and Methods), which is also consistent with a recently published phylogenetic study (Vidal and Hedges 2009). *represents detection of COX8 in the genome sequence of the relevant organism.
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evt131-F3: Schematic phylogenetic tree demonstrating the presence or absence of COX8 across the vertebrate phylogeny. Letters above each branch indicate the presence of the relevant COX8 isoforms. Non: total absence of all COX8 isoforms. Notably, the suborders Iguania and Serpentes are labeled. The topology of the tree is adopted from NCBI Taxonomy (see URL in Material and Methods), which is also consistent with a recently published phylogenetic study (Vidal and Hedges 2009). *represents detection of COX8 in the genome sequence of the relevant organism.

Mentions: Because the most complete set of nDNA-encoded OXPHOS genes was mainly studied and recorded in humans, we created a local Blast database from 86 human nDNA-encoded OXPHOS structural subunits (including subunit isoforms) and compared all available transcriptome sequences with this database. The majority of the human OXPHOS genes had orthologs in the transcriptomes of most studied organisms, whereas the M. gallopavo (Turkey) transcriptome yielded the lowest amount of orthologs (56) (fig. 2), possibly reflecting missing data in that organism. This explanation could apply to other species with lower numbers of identified OXPHOS orthologs. In the C. chamaeleon transcriptome we identified 78 human orthologs (including isoforms), an amount similar to the other recently sequenced reptilian transcriptomes. The most prominent finding was the lack of COX8 (including its human isoforms) in all reptile transcriptomes, excluding the crocodile, which is phylogenetically closer to birds than to other reptiles (Gauthier et al. 1989). When we extended our database search to find additional COX8 isoforms using the mouse COX8B sequence as a reference, we identified COX8B orthologs in all tested Serpentes (snakes), T. elegans, P. molurus bivittatus, and E. guttata, but not in the examined iguanian lizards, C. chamaeleon, A. Carolinensis, and Pog. vitticeps, as well as the terrapin Tra. scripta (fig. 3).Fig. 2.—


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)

Schematic phylogenetic tree demonstrating the presence or absence of COX8 across the vertebrate phylogeny. Letters above each branch indicate the presence of the relevant COX8 isoforms. Non: total absence of all COX8 isoforms. Notably, the suborders Iguania and Serpentes are labeled. The topology of the tree is adopted from NCBI Taxonomy (see URL in Material and Methods), which is also consistent with a recently published phylogenetic study (Vidal and Hedges 2009). *represents detection of COX8 in the genome sequence of the relevant organism.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evt131-F3: Schematic phylogenetic tree demonstrating the presence or absence of COX8 across the vertebrate phylogeny. Letters above each branch indicate the presence of the relevant COX8 isoforms. Non: total absence of all COX8 isoforms. Notably, the suborders Iguania and Serpentes are labeled. The topology of the tree is adopted from NCBI Taxonomy (see URL in Material and Methods), which is also consistent with a recently published phylogenetic study (Vidal and Hedges 2009). *represents detection of COX8 in the genome sequence of the relevant organism.
Mentions: Because the most complete set of nDNA-encoded OXPHOS genes was mainly studied and recorded in humans, we created a local Blast database from 86 human nDNA-encoded OXPHOS structural subunits (including subunit isoforms) and compared all available transcriptome sequences with this database. The majority of the human OXPHOS genes had orthologs in the transcriptomes of most studied organisms, whereas the M. gallopavo (Turkey) transcriptome yielded the lowest amount of orthologs (56) (fig. 2), possibly reflecting missing data in that organism. This explanation could apply to other species with lower numbers of identified OXPHOS orthologs. In the C. chamaeleon transcriptome we identified 78 human orthologs (including isoforms), an amount similar to the other recently sequenced reptilian transcriptomes. The most prominent finding was the lack of COX8 (including its human isoforms) in all reptile transcriptomes, excluding the crocodile, which is phylogenetically closer to birds than to other reptiles (Gauthier et al. 1989). When we extended our database search to find additional COX8 isoforms using the mouse COX8B sequence as a reference, we identified COX8B orthologs in all tested Serpentes (snakes), T. elegans, P. molurus bivittatus, and E. guttata, but not in the examined iguanian lizards, C. chamaeleon, A. Carolinensis, and Pog. vitticeps, as well as the terrapin Tra. scripta (fig. 3).Fig. 2.—

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