Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes

Abstract

The first two mitochondrial genomes of marine diatoms were previously reported for the centric Thalassiosira pseudonana and the raphid pennate Phaeodactylum tricornutum. As part of a genomic project, we sequenced the complete mitochondrial genome of the freshwater araphid pennate diatom Synedra acus. This 46,657 bp mtDNA encodes 2 rRNAs, 24 tRNAs, and 33 proteins. The mtDNA of S. acus contains three group II introns, two inserted into the cox1 gene and containing ORFs, and one inserted into the rnl gene and lacking an ORF. The compact gene organization contrasts with the presence of a 4.9-kb-long intergenic region, which contains repeat sequences. Comparison of the three sequenced mtDNAs showed that these three genomes carry similar gene pools, but the positions of some genes are rearranged. Phylogenetic analysis performed with a fragment of the cox1 gene of diatoms and other heterokonts produced a tree that is similar to that derived from 18S RNA genes. The introns of mtDNA in the diatoms seem to be polyphyletic. This study demonstrates that pyrosequencing is an efficient method for complete sequencing of mitochondrial genomes from diatoms, and may soon give valuable information about the molecular phylogeny of this outstanding group of unicellular organisms.

A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of theBerkeleya rutilanscomplex (Bacillariophyceae)

“…The SSU and UPA markers have broad applicability across protistan taxa and can be easily used in environmental surveys (Godhe et al, 2008;Sherwood et al, 2008), but cannot distinguish between closely related species and therefore are not the best markers for uncovering diatom diversity (Moniz & Kaczmarska, 2009;Hamsher et al, 2011;Zimmerman et al, 2011). The COI-5P region is able to distinguish between diatom species, but cannot be easily amplified and sequenced for some diatom lineages (Hamsher et al, 2011), possibly due to introns in the region (Armbrust et al, 2004;Ravin et al, 2010). A region (780 bp) towards the 3′ end of the rbcL (rbcL-3P) and the variable D2/D3 region of the LSU (LSU D2/D3) have recently been suggested as species-level markers for diatoms (Hamsher et al, 2011).…”

Complete Chloroplast Genome Sequence of Freshwater Araphid Pennate Diatom Alga Synedra acus from Lake Baikal

“…Diatom cells were collected on a filter with 5 μm pores and washed with sterile medium. Total DNA was isolated as in Ravin et al (2010).…”

“…In Lake Baikal, eventual under-ice blooms of S. acus have been reported to feed zooplankton and left records in Pleistocene and Holocene sediments of Lake Baikal (Grachev et al 1998). Like with the mitochondrial genome of S. acus (Ravin et al 2010), we used total DNA isolation procedure followed by shot-gun pyrosequencing to decipher its chloroplast DNA (cpDNA).…”

A procedure for establishing an axenic culture of the diatom Synedra acus subsp. radians (Kütz.) Skabibitsch. from Lake Baikal

“…In addition, they were tested by PCR for amplification of a bacterial 16S rRNA gene fragment. With this purpose, diatoms were collected on a polycarbonate membrane with a pore size of 1 µm (Millipore) and immediately used to isolate DNA by the method described previously (Ravin et al 2010). The DNA samples were used as templates for PCR with universal bacterial primers 500 L 5¢-CGTGCCAGCAGCCGCGGTAA-3¢ and 1350R 5¢-GACGGGCG-GTGTGTACAAG-3¢, which amplified a 850-bp 16S rRNA gene fragment.…”

“…radians (Kütz.) Skabitsch., one of the dominant species in the phytoplankton of Lake Baikal, has been the object of research on morphogenesis of diatom frustules (Kaluzhnaya and Likhoshway 2007) as well as of molecular biological (Grachev et al 2002;Sherbakova et al 2005;Petrova et al 2007), cytological (Bedoshvili et al 2009), and genomic studies (Ravin et al 2010). Our purpose was to develop a procedure for establishing an axenic culture of this diatom.…”