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

Yuri P Galachyants,Darya P Petrova,Andrey V Mardanov,Nikolay V Ravin,Yelena V Likhoshway,Alexey V Beletsky,Alexey A Morozov

doi:10.5539/ijb.v4n1p27

Abstract

Complete chloroplast genome of diatom alga Synedra acus possesses canonical quadripartite structure with two inverted repeats containing ribosomal RNA gene loci that separate small and large single-copy regions. Chloroplast genome maps as a circular molecule of 116 251 bp. It encodes 27 tRNAs, three rRNAs, two small RNA genes, and 128 protein-coding genes. Comparison of the genic features across diatom chloroplast genomes reveals the absence of an overlap between atpD and atpF gene coding sequences that is present in other plastid genomes of diatom origin. This feature is a clear synapomorphy of S. acus plastid genome that is likely a result of either relaxed constraints or extensive selection forces acting upon atpF gene. We also characterized nuclear-encoded acyl-carrier protein gene with chloroplastic targeting in S. acus . The transfer of acpp gene into the nuclear host genome is hypothesized to have occurred independently in several lineages of diatoms.

Highlights

Diatom algae are a group of unicellular eukaryotes, which is one of the major photosynthetic producers of organic carbon in the world, providing about 20% of net primary production (Falkowski et al 2004)
This chloroplast DNA (cpDNA) is compared to other chloroplast genomes of diatom origin to integrate the newly available data into the overall concept of the plastid genomics of diatoms
Plastid genome of S. acus is somewhat smaller than those of other diatom algae sequenced to date, whereas other general features of the genome such as GC-content and coding capacity are very similar between cpDNAs of diatoms/dinotoms group

Summary

Introduction

Diatom algae are a group of unicellular eukaryotes, which is one of the major photosynthetic producers of organic carbon in the world, providing about 20% of net primary production (Falkowski et al 2004). Chloroplast of diatoms had initially a cyanobacterial origin and was inherited from an ancient red alga during its secondary endosymbiosis with a heterotrophic eukaryote. Diatoms inhabit almost all water environments, from marine to ultra-oligotrophic freshwater bodies and from pack-ice to thermal springs (Round et al 1997). The present number of diatom species is reported to be up to 105-106 including cryptic ones (Round et al 1997). Based on cell wall symmetry and other morphological features, diatoms could be separated into several large groups which are listed in the order of their divergence: radial and bipolar centrics, araphids, and raphid pennates, with only the last group believed to be monophyletic (Sims et al 2006)

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Conclusion