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Inferring the phylogeny of bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes.

ABSTRACT: Molecular techniques that assess biodiversity through the analysis of a small segment of mitochondrial genome have been getting wide attention for inferring the mammalian diversity. Due to their highly conserved nature, specific mitochondrial genes offer a promising tool for phylogenetic analysis. However, there is no established criteria for selecting the typical mitochondrial DNA (mtDNA) segments to achieve a greater resolving power. We therefore chose the family Bovidae as a model and compared the tree-topologies resulting from the commonly used and phylogenetically-informative genes including 16S rRNA, 12S rRNA, COI, Cyt b and D-loop with respect to complete mitochondrial genome. The tree topologies from the whole mitochondrial genome of 12 species were not identical albeit similar with those resulting from the five individual genes mentioned above. High bootstrap values were observed for mtDNA compared with that of any single gene. The average pair-wise sequence divergence using different genetic modes was found to be: D-loop (0.229) > Cyt b (0.159) > COI or complete mtDNA (0.143) > 12S rRNA (0.094) > 16S rRNA (0.091). The tree resulting from complete mtDNA clearly separated the 12 taxa of Bovidae into 3 major clusters, one cluster each for subfamily Cervinae and Bovinae and the third cluster comprised the distinctive clades of Caprinae and Antilopinae. However, jumping clades of Antilopinae were observed while using the individual genes. This study showed that Bison bison and Bos Taurus have very close phylogenetic relationship compared to Bubalus bubalis (Bovinae), irrespective of the method used. Our findings suggest that complete mtDNA genome provides most reliable understanding of complex phylogenetic relationships while the reliability of individual gene trees should be verified with high bootstrap support.

SUBMITTER: Arif IA

PROVIDER: S-EPMC3290115 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Inferring the phylogeny of bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes.

Arif Ibrahim A IA Bakir Mohammad A MA Khan Haseeb A HA

Evolutionary bioinformatics online 20120220

Molecular techniques that assess biodiversity through the analysis of a small segment of mitochondrial genome have been getting wide attention for inferring the mammalian diversity. Due to their highly conserved nature, specific mitochondrial genes offer a promising tool for phylogenetic analysis. However, there is no established criteria for selecting the typical mitochondrial DNA (mtDNA) segments to achieve a greater resolving power. We therefore chose the family Bovidae as a model and compare ...[more]

PMID: 22399841

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Project description:BACKGROUND:Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS:We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS:Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads?+?Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales?+?Psilotales are sister to Marattiales?+?leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.

Project description:BackgroundThe genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse.ResultsWe conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis.ConclusionsThis study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.

Dataset Information

Inferring the phylogeny of bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes.

Publications

Inferring the phylogeny of bovidae using mitochondrial DNA sequences: resolving power of individual genes relative to complete genomes.

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