The complete chloroplast genome of the marine araphid diatom Nanofrustulum shiloi

Chunlian Li1,2, Romain Gastineau2, Andrzej Witkowski2, Monique Turmel1, Przemysław Dąbek2 and Claude Lemieux1

1   Departement de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Laval University, Canada and

 2   Palaeoceanology Unit, Faculty of Geosciences, University of Szczecin, Poland

To better understand the broad-scale evolutionary pattern of the chloroplast genome in diatoms, we sampled the widely distributed, bloom-forming marine diatom Nanofrustulum shiloi (diameter ranging from 2.5 to 5.5 µm). The chloroplast genome of this minute alga maps as a circular molecule of 160,994 bp and displays an inverted repeat of 11,617 bp. It codes for 128 proteins, 3 rRNAs, 27 tRNAs, tmRNA and Ffs RNA, for a total of 160 gene products. All of these genes are also found in previously sequenced diatom chloroplast genomes. We compared the chloroplast gene organization of N. shiloi with those of four other pennate diatoms: two araphids (Asterionella Formosa and Asterionellopsis glacialis) and two raphids (Eunotia naegelii and Phaeodactylum tricornutum). Surprisingly, the araphid N. shiloi showed more similarity in gene order with the two raphids than the araphids. A group II intron was discovered in the N. shiloi petB gene, which codes for a reverse transcriptase/maturase similar to that encoded by a group II intron found in the cyanobacterium Lyngbya sp. Moreover, within the 11.6-kb region located between psaJ and psaA, we identified multiple hypothetical ORFs matching sequences that are present in plasmids of other diatoms.