Sequencing of the complete genome of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal

Abstract

High-throughput method of sequencing was applied to determine the complete nucleotide sequence of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal (East Siberia). The assembled genome has a total length of 98 Mbp, the mean coverage is 33x. Structure-functional annotation of the genome was performed.

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

“…First, the complete protein libraries annotated from eleven ochrophyte genomes (the diatoms Phaeodactylum tricornutum (Bowler et al, 2008), Thalassiosira pseudonana (Armbrust et al, 2004), Thalassiosira oceanica (Lommer et al, 2012), Fistulifera solaris (Tanaka et al, 2015b), Fragilariopsis cylindrus, Synedra acus (Galachyants et al, 2015), and Pseudonitzschia multiseries ; the pelagophyte Aureococcus anophagef ferens (Gobler et al, 2011); the eustigmatophytes Nannochloropsis gaditana and Nannochloropsis salina (Radakovits et al, 2013; Wang et al, 2014); and the kelp Ectocarpus siliculosus (Cock et al, 2010); Table S1- sheet 1 [Dorrell et al, 2016]), were screened using the ochrophyte plastid-targeting predictors ASAFind (Gruber et al, 2015) (used in conjunction with SignalP version 3.0 (Bendtsen et al, 2004); Table S2 [Dorrell et al, 2016]) and HECTAR (Gschloessl et al, 2008) (integrated into a Galaxy (Afgan et al, 2016) instance available at http://webtools.sb-roscoff.fr; Table S3 [Dorrell et al, 2016]). All proteins that were deemed to possess plastid-targeting sequences (regardless of the confidence score applied by ASAFind [Gruber et al, 2015]) were retained for further inspection.…”

Systematic and functional analysis of horizontal gene transfer events in diatoms

“…9 classes sorted from young to old and per origin in four diatoms. The number of genes is indicated in 26 between brackets. The asterisks denote a statistical difference per type within the same age category 27 and have the following confidence range for p-values; * : 0.05, ** : 0.01, *** : 0.001, ****: 0.0001.…”

“…In the early 22 Cretaceous, between 150 and 130 million years ago, diatoms split into the centric and pennate lineage. 23 Several whole-genome sequences of representatives from polar centrics (Thalassiosira pseudonana 23 , 24 Thalassiosira oceanica 24 , Cyclotella cryptica 25 ), araphid pennates (Synedra acus 26 ) and raphid pennates 25 (Phaeodactylum tricornutum 7,27 , Fistulifera solaris 28 , Fragilariopsis cylindrus 29 , Pseudo-nitzschia 26 multistriata 30 ) have become available in recent years, which allows the analysis of the evolutionary 27 history within diatoms. It is not fully understood how HGT has contributed to the ecological success of 28 this environmentally important group of organisms.…”

TheSeminavis robustagenome provides insights into the evolutionary adaptations of benthic diatoms

“…More recent studies have extended our knowledge of the complexity of diatom genomes, some examples being the oleaginous pennate Fistulifera solaris [11] with an allodiploid genome structure and the cold-adapted pennate Fragilariopsis cylindrus with a highly heterozygous genome showing allele-specific expression in response to environmental stresses [12]. While these first diatom genomes were small , sequencing of diatoms with larger genomes, including the centric Thalassiosira oceanica (92 Mb) [13] and the araphid pennate Synedra acus (98 Mb, also named Fragilaria radians) [14], have shown that these species have more than twice the number of protein-coding genes than the two first sequenced diatoms (T. pseudonana and P. tricornutum), suggesting the traditional diatom models are underestimating gene diversity.…”