Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Abstract

Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.

Genome-Wide Identification, Molecular Characterization, and Involvement in Response to Abiotic and Biotic Stresses of the HSP70 Gene Family in Turbot (Scophthalmus maximus)

“…To identify the full set of HSP70 genes in the turbot, the genome sequence, annotation file, and protein sequences of the turbot were first collected from NCBI databases (GCA_022379125.1) [ 33 ]. Then, two strategies were used to search the turbot genome to identify HSP70 genes.…”

“…Because of the essential functions of HSP70 genes in response to diverse stresses, systematically identifying and exploring their expression patterns under abiotic and biotic stresses is expected to be valuable for further functional studies and exhibit important practical significance in the development of efficient farming practices, thereby leading to an increase in turbot fitness in aquaculture production. Fortunately, high-quality genome assembly [ 33 ] and multiple published RNA-seq datasets resources [ 26 , 27 , 28 , 30 , 31 , 32 , 34 , 35 ] made available in recent years make it possible to perform systematic identification, phylogenetic analysis, and a functional study of HSP70 genes in the turbot.…”

Genome-Wide Identification and Involvement in Response to Biotic and Abiotic Stresses of lncRNAs in Turbot (Scophthalmus maximus)

“…First, fastq-dump tool of SRAtoolkit software was used to convert the RNA-seq datasets downloaded in SRA format into FASTQ format [77]. Then, reads were aligned with the latest assembled turbot genome (GCA_022379125.1 [50]) using STAR software version 2.7.11a [78] with default parameters. To find new splice junctions, a two-pass alignment for each read was run using STAR with the parameter "--sjdbFileChrStartEnd".…”

“…These environmental stresses severely threatened the healthy and survival of turbot, which has led to enormous economic losses to the turbot aquaculture industry and greatly hindered the health and sustainable development of the turbot aquaculture industry. A large number of studies have been conducted on the changes in gene expression under various environmental stresses in recent years [48][49][50]. However, there has been no systematic identification and characterization of lncRNAs in turbot and no adequate detection of their roles in response to abiotic and biotic stress in turbot up to now.…”

“…However, there has been no systematic identification and characterization of lncRNAs in turbot and no adequate detection of their roles in response to abiotic and biotic stress in turbot up to now. Fortunately, abundant available RNA-seq dataset resources [40][41][42][43][45][46][47]51,52] and highquality turbot genome sequences [50] make it possible to conduct systematic identification, characterization, and functional study of lncRNAs in the turbot.…”