Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

Abstract

Schizochytrium sp. is the best natural resource for omega-3 long-chain polyunsaturated fatty acids. We report a high-quality genome sequence of Schizochytrium limacinum SR21, which has a 63 Mb genome size, with a contig N50 of 2.67 Mb and 6,838 protein-coding genes. Phylogenomic and comparative genomic analyses revealed that DHA-producing Schizochytrium and Aurantiochytrium strains were highly similar and possessed similar genes. Analysis of the fatty acid synthase (FAS) for LC-PUFAs production results in the annotation of all genes in map00062 and map01212. A gene cluster and 10 ORFs related to PKS pathway were found in the genome. 1,402 differentially expressed genes (DEGs) of the treated groups (0.5 g/L yeast extract) were identified by comparing with the control groups (1.0 g/L yeast extract) at 36 h. A weighted gene coexpression network analysis revealed that 2 of 7 modules correlated highly with the fatty acid and DHA contents. The DEGs and transcription factors were significantly correlated with fatty acid biosynthesis, including MYB, Zinc Finger and ACOX. The results showed that these hub genes are regulated by genes involved in fatty acid biosynthesis pathways. The results providing an important reference for further research on promoting fatty acid and DHA accumulation in S. limacinum SR21.

Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii

“…Genus Thraustochytrium clusters more compactly but also do not form a separate monophyletic group. Our phylogenetic reconstruction of the Thraustochytriaceae species is in agreement with the previous data ( Caamaño et al, 2017 ), and also points out the necessity of the revision of the family Thraustochytriaceae taxonomy ( Dellero et al, 2018 ; Ju et al., 2019 ; Liang et al., 2019 ). Special attention should be given to genera Schizochytrium and Aurantiochytrium as their representatives are dispersedly distributed around the oceans.…”

“…This species forms an outgroup to T. kinnei in the phylogenetic tree. The other representatives of the genus Schizochytrium do not form one clade, raising doubts about their belonging to the same genus ( Dellero et al, 2018 ; Ju et al., 2019 ; Liang et al., 2019 ). Genus Thraustochytrium clusters more compactly but also do not form a separate monophyletic group.…”

“…We were not able to distinguish between T. aureum and T. roseum by 18S rRNA. Notably, clusterization of the 18S rRNA sequences had not been measured against their species taxonomic position, thus making necessary a previously proposed revision of the family Thraustochytriaceae systematics ( Andersen & Ganuza, 2018 ; Yokoyama & Honda, 2007 ; Ju et al., 2019 ; Liang et al., 2019 ). Our transcriptome data on Thraustochytrium close the significant gap in the taxon Thraustochytriaceae.…”

“…Probably there are several genetically diverse though morphologically similar species ( Yokoyama & Honda, 2007 ). The use of both 18S rRNA sequences and whole-genome data should clarify their systematic position ( Liang et al., 2019 ; Ju et al., 2019 ).…”

A non-canonical Δ9-desaturase synthesizing palmitoleic acid identified in the thraustochytrid Aurantiochytrium sp. T66

“…One of the reasons that thraustochytrids may not usually generate DHA through the DE pathway is that many strains are missing one or more of the expected DE pathway desaturases and elongases (Dellero et al 2018 ; Liang et al 2020 ; Meesapyodsuk and Qiu 2016 ). For example, here we demonstrated that Aurantiochytrium sp.…”