Abstract
BackgroundThe mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).MethodsMitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.ResultsThe G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.ConclusionThese results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1988-0) contains supplementary material, which is available to authorized users.
Highlights
IntroductionTo elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.)
The mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced
Comparative analysis of G. barbadense and G. hirsutum mitochondrial genomes The mitochondrial genomes of G. barbadense and G. hirsutum [41] are largely similar; as observed in other genera, many differences exist even between these closely related species (Table 1)
Summary
To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.). Plant mitochondrial genomes are remarkable from both evolutionary and comparative genomics stand-points. Like their animal counterparts, plant mitochondrial genomes generally are characterized as circular chromosomes [1] (barring notable exceptions, e.g., [2, 3]) that contain a variable number of genes interspersed within non-coding DNA; this simplistic generalization belies the dynamic and complex nature of plant mitochondrial. Plant mitochondrial genomes vary remarkably both in size and composition within plant families and genera [7, 9, 16, 17], with genome sizes ranging from 30 kilobases in some algae to several megabases in certain angiosperms [2, 3, 18]. Plant mitochondrial genomes vary by an amazing 870fold, from the ultra-compact, 12 kb (12,998 bp) genome (Accession Number: NC 010357) of the alga Polytomella
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