Abstract
BackgroundThe variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among closely related genera. However, sampling of mt genomes on a within-family scale is still poor and the sparsity of information precludes a thorough understanding of genome evolution in the green algae.MethodsGenomic DNA of representative taxa were sequenced on an Illumina HiSeq2500 to produce 2x100 bp paired reads, and mitochondrial genomes were assembled and annotated using Geneious v.6.1.5. Phylogenetic analysis of 13 protein-coding mitochondrial genes spanning the Sphaeropleales was performed.ResultsThis study presents one of the first within-family comparisons of mt genome diversity, and is the first to report complete mt genomes for the family Hydrodictyaceae (order Sphaeropleales). Four complete mt genomes representing three taxa and four phylogenetic groups, Stauridium tetras, Pseudopediastrum boryanum, and Pediastrum duplex, range in size from 37,723 to 53,560 bp. The size variability is primarily due to intergenic region expansion, and intron content is generally low compared with other mt genomes of Sphaeropleales.ConclusionsCertain gene rearrangements appear to follow a phylogenetic pattern, and with a more thorough taxon sampling genome-level sequence may be useful in resolving systematic conundrums that plague this morphologically diverse family.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2056-5) contains supplementary material, which is available to authorized users.
Highlights
The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale
To contribute to the sampling of mt genomes in Sphaeropleales and test the phylogenetic patterns of gene arrangements and genome architecture within a family, we offer four fully assembled hydrodictyacean mt genomes, as well as protein-coding gene sequences from the fragmentary mt assembly of Hydrodictyon reticulatum
Data collection resulted in 9.8 million reads for Stauridium tetras [GenBank:KR026341], 11.1 million reads for Pseudopediastrum boryanum [GenBank:KR026342], 8.7 million reads obtained for Pediastrum duplex AL0403MN [GenBank:KR026339], and 7.6 million reads for Pediastrum duplex PL0501b [GenBank:KR026340]
Summary
The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among closely related genera. Mitochondrial genomes of Viridiplantae, outside of land plants, have been largely understudied. Being the closest relatives to land plants, studying the evolution of streptophyte algae has prompted the sequencing of multiple genomes from charophycean lineages [1,2,3,4,5]. Nine mt genomes were sequenced from the sister group of Volvocales, the order Sphaeropleales, previously characterized by only Acutodesmus obliquus [7, 8]. Through phylogenetic analyses and examination of gene rearrangement and intron content, variation was seen across the sampling of Sphaeropleales.
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