Limits...
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.

Show MeSH

Related in: MedlinePlus

Orthologs of nDNA-encoded OXPHOS human genes in 34 vertebrate transcriptomes. Red box: missing ortholog. Blue box: ortholog identified only in the whole genome sequence of the relevant species*. Framed in yellow: missing COX8 in iguanian lizards. Green background: reptilian species. Species name abbreviations: HS, Homo sapiens; PT, Pan troglodytes; PA, Pongo abelii; NL, Nomascus leucogenys; MM, Macaca mulatta; CJ, Callithrix jacchus; SS, Sus scrofa; BT, Bos taurus; EC, Equus caballus; LA, Loxodonta africana; AM, Ailuropoda melanoleuca; CL, Canis lupus familiaris; MS, Mus musculus; RN, Rattus norvegicus; CG, Cricetulus griseus; CP, Cavia porcellus; OC, Oryctolagus cuniculus; MD, Monodelphis domestica; OA, Ornithorhynchus anatinus; CC, Chamaeleo chamaeleon; AC, Anolis carolinensis; PV, Pogona vitticeps; TE, Thamnophis elegans; EG, Elaphe guttata; PM, Python molurus bivittatus; TS, Trachemys scripta; CN, Crocodylus niloticus; GG, Gallus gallus; TG, Taeniopygia guttata; MG, Meleagris gallopavo; XT, Xenopus (silurana) tropicalis; DR, Danio rerio; ON, Oreochromis niloticus; TN, Tetraodon nigroviridis; FR, Fugu rubripes. *NCBI genome sequences were not available for the following species: CC, PV, TE, EG, PM, TS, CN, and TN. **Cox8b sequence was extracted from a mouse reference as it was absent in humans.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3814190&req=5

evt131-F2: Orthologs of nDNA-encoded OXPHOS human genes in 34 vertebrate transcriptomes. Red box: missing ortholog. Blue box: ortholog identified only in the whole genome sequence of the relevant species*. Framed in yellow: missing COX8 in iguanian lizards. Green background: reptilian species. Species name abbreviations: HS, Homo sapiens; PT, Pan troglodytes; PA, Pongo abelii; NL, Nomascus leucogenys; MM, Macaca mulatta; CJ, Callithrix jacchus; SS, Sus scrofa; BT, Bos taurus; EC, Equus caballus; LA, Loxodonta africana; AM, Ailuropoda melanoleuca; CL, Canis lupus familiaris; MS, Mus musculus; RN, Rattus norvegicus; CG, Cricetulus griseus; CP, Cavia porcellus; OC, Oryctolagus cuniculus; MD, Monodelphis domestica; OA, Ornithorhynchus anatinus; CC, Chamaeleo chamaeleon; AC, Anolis carolinensis; PV, Pogona vitticeps; TE, Thamnophis elegans; EG, Elaphe guttata; PM, Python molurus bivittatus; TS, Trachemys scripta; CN, Crocodylus niloticus; GG, Gallus gallus; TG, Taeniopygia guttata; MG, Meleagris gallopavo; XT, Xenopus (silurana) tropicalis; DR, Danio rerio; ON, Oreochromis niloticus; TN, Tetraodon nigroviridis; FR, Fugu rubripes. *NCBI genome sequences were not available for the following species: CC, PV, TE, EG, PM, TS, CN, and TN. **Cox8b sequence was extracted from a mouse reference as it was absent in humans.

Mentions: We downloaded from NCBI all the available RefSeq transcripts of Pan troglodytes, Pongo abelii, Nomascus leucogenys, Macaca mulatta, Callithrix jacchus, Sus scrofa, Bos taurus, Equus caballus, Loxodonta africana, Ailuropoda melanoleuca, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Cricetulus griseus, Cavia porcellus, Oryctolagus cuniculus, Monodelphis domestica, Ornithorhynchus anatinus, A. carolinensis, Taeniopygia guttata, Gallus gallus, Meleagris gallopavo, Xenopus (silurana) tropicalis, Danio rerio, and Oreochromis niloticus. We also downloaded available assembled transcripts from recently sequenced vertebrates, including Thamnophis elegans, Python molurus bivittatus, Pogona vitticeps, Elaphe guttata, Trachemys scripta, Crocodylus niloticus, G. gallus, Tetraodon nigroviridis, Fugu rubripes (Jaillon et al. 2004; Schwartz et al. 2010; Castoe et al. 2011; Kai et al. 2011; Tzika et al. 2011). Notably, the recently sequenced G. gallus transcriptome gave better results than the available RefSeq transcripts; therefore we used those transcripts in further analysis. We then downloaded 86 known human nDNA-encoded OXPHOS proteins sequences and constructed a local Blast database (Blast 2.2.25+ [Altschul et al. 1997]). Blast screen was performed for each transcriptome against the OXPHOS human genes to identify orthologs. A contig was considered a hit if its similarity value was above 1.0E−5, following recently used threshold (Schwartz et al. 2010; Castoe et al. 2011). Additionally, for each OXPHOS subunit, only contigs having the lowest e-value were further analyzed. Then, in order to exhaust all publicly available data, an additional Blast (TBlastN, BlastP, and BlastN) search was performed for each of the species in which we analyzed RefSeq transcripts, using the entire NCBI database (nr) and all available genomes in NCBI. Figure 2 specifies the identification of each subunit in the transcriptomes and (when available) genomes of each species.


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)

Orthologs of nDNA-encoded OXPHOS human genes in 34 vertebrate transcriptomes. Red box: missing ortholog. Blue box: ortholog identified only in the whole genome sequence of the relevant species*. Framed in yellow: missing COX8 in iguanian lizards. Green background: reptilian species. Species name abbreviations: HS, Homo sapiens; PT, Pan troglodytes; PA, Pongo abelii; NL, Nomascus leucogenys; MM, Macaca mulatta; CJ, Callithrix jacchus; SS, Sus scrofa; BT, Bos taurus; EC, Equus caballus; LA, Loxodonta africana; AM, Ailuropoda melanoleuca; CL, Canis lupus familiaris; MS, Mus musculus; RN, Rattus norvegicus; CG, Cricetulus griseus; CP, Cavia porcellus; OC, Oryctolagus cuniculus; MD, Monodelphis domestica; OA, Ornithorhynchus anatinus; CC, Chamaeleo chamaeleon; AC, Anolis carolinensis; PV, Pogona vitticeps; TE, Thamnophis elegans; EG, Elaphe guttata; PM, Python molurus bivittatus; TS, Trachemys scripta; CN, Crocodylus niloticus; GG, Gallus gallus; TG, Taeniopygia guttata; MG, Meleagris gallopavo; XT, Xenopus (silurana) tropicalis; DR, Danio rerio; ON, Oreochromis niloticus; TN, Tetraodon nigroviridis; FR, Fugu rubripes. *NCBI genome sequences were not available for the following species: CC, PV, TE, EG, PM, TS, CN, and TN. **Cox8b sequence was extracted from a mouse reference as it was absent in humans.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evt131-F2: Orthologs of nDNA-encoded OXPHOS human genes in 34 vertebrate transcriptomes. Red box: missing ortholog. Blue box: ortholog identified only in the whole genome sequence of the relevant species*. Framed in yellow: missing COX8 in iguanian lizards. Green background: reptilian species. Species name abbreviations: HS, Homo sapiens; PT, Pan troglodytes; PA, Pongo abelii; NL, Nomascus leucogenys; MM, Macaca mulatta; CJ, Callithrix jacchus; SS, Sus scrofa; BT, Bos taurus; EC, Equus caballus; LA, Loxodonta africana; AM, Ailuropoda melanoleuca; CL, Canis lupus familiaris; MS, Mus musculus; RN, Rattus norvegicus; CG, Cricetulus griseus; CP, Cavia porcellus; OC, Oryctolagus cuniculus; MD, Monodelphis domestica; OA, Ornithorhynchus anatinus; CC, Chamaeleo chamaeleon; AC, Anolis carolinensis; PV, Pogona vitticeps; TE, Thamnophis elegans; EG, Elaphe guttata; PM, Python molurus bivittatus; TS, Trachemys scripta; CN, Crocodylus niloticus; GG, Gallus gallus; TG, Taeniopygia guttata; MG, Meleagris gallopavo; XT, Xenopus (silurana) tropicalis; DR, Danio rerio; ON, Oreochromis niloticus; TN, Tetraodon nigroviridis; FR, Fugu rubripes. *NCBI genome sequences were not available for the following species: CC, PV, TE, EG, PM, TS, CN, and TN. **Cox8b sequence was extracted from a mouse reference as it was absent in humans.
Mentions: We downloaded from NCBI all the available RefSeq transcripts of Pan troglodytes, Pongo abelii, Nomascus leucogenys, Macaca mulatta, Callithrix jacchus, Sus scrofa, Bos taurus, Equus caballus, Loxodonta africana, Ailuropoda melanoleuca, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Cricetulus griseus, Cavia porcellus, Oryctolagus cuniculus, Monodelphis domestica, Ornithorhynchus anatinus, A. carolinensis, Taeniopygia guttata, Gallus gallus, Meleagris gallopavo, Xenopus (silurana) tropicalis, Danio rerio, and Oreochromis niloticus. We also downloaded available assembled transcripts from recently sequenced vertebrates, including Thamnophis elegans, Python molurus bivittatus, Pogona vitticeps, Elaphe guttata, Trachemys scripta, Crocodylus niloticus, G. gallus, Tetraodon nigroviridis, Fugu rubripes (Jaillon et al. 2004; Schwartz et al. 2010; Castoe et al. 2011; Kai et al. 2011; Tzika et al. 2011). Notably, the recently sequenced G. gallus transcriptome gave better results than the available RefSeq transcripts; therefore we used those transcripts in further analysis. We then downloaded 86 known human nDNA-encoded OXPHOS proteins sequences and constructed a local Blast database (Blast 2.2.25+ [Altschul et al. 1997]). Blast screen was performed for each transcriptome against the OXPHOS human genes to identify orthologs. A contig was considered a hit if its similarity value was above 1.0E−5, following recently used threshold (Schwartz et al. 2010; Castoe et al. 2011). Additionally, for each OXPHOS subunit, only contigs having the lowest e-value were further analyzed. Then, in order to exhaust all publicly available data, an additional Blast (TBlastN, BlastP, and BlastN) search was performed for each of the species in which we analyzed RefSeq transcripts, using the entire NCBI database (nr) and all available genomes in NCBI. Figure 2 specifies the identification of each subunit in the transcriptomes and (when available) genomes of each species.

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