Comprehensive Transcriptome Analysis Reveals Insights into Phylogeny and Positively Selected Genes of Sillago Species

Whole transcriptome analysis of demersal fish eggs reveals complex responses to ocean deoxygenation and acidification

Ocean acidification and deoxygenation co-occur in marine environments, causing deterioration of marine ecosystems. However, effects of compound stresses on marine organisms and their physiological coping mechanisms are largely unknown. Here, we show how high pCO2 and low dissolved oxygen (DO) cause transcriptomic changes in eggs of a demersal fish (Sillago japonica), which are fully exposed to such stresses in natural environment. Overall gene expression was affected more strongly by low DO than by high pCO2. Enrichment analysis detected significant stress responses such as glycolytic processes in response to low DO. Increased expression of a group of glycolytic genes under low DO conditions is presumably because oxygen depletion disables the electron transfer pathway, complementing ATP production in the glycolytic pathway. Contrary to expectations, apparent mitigation of gene expression changes was dominant under combined stress conditions, and may represent an innate fish adaptive trait for severe environments.

Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica

As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.

Comprehensive phylogeny of Konosirus punctatus (Clupeiformes: Clupeidae) based on transcriptomic data

Konosirus punctatus is an important species for the structure of marine ecosystems. Meanwhile, it is a native species in the northwest Pacific Ocean and supports important commercial fishery. In the present study, we generated the whole transcriptome of K. punctatus from combined tissues (muscle, liver, gill, heart, kidney, swim bladder and sexual gland) using Illumina RNA-seq technology and a total of 46087110 clean reads were obtained, corresponding to 6531521430 nucleotides. Meanwhile, 10000 clean reads were randomly selected and compared with NT database to examine the possible contamination. Results showed that 6754 clean reads were distributed among some species closely related with K. punctatus, indicating no-pollution. De novo assembly was performed and all clean reads were assembled to produce 71610 longest unigenes with an N50 of 906 bp. Among all the unigenes, 43974 unigenes were annotated in at least one database and 3172 unigenes were annotated in all databases. All unigenes were further analyzed to predict the gene structure and we have obtained a total of 54864 coding sequences (CDSs) and 17326 simple sequence repeats (SSRs). Saturation analyses were applied to evaluate the accuracy of gene expression and we hypothesized that the detection of gene expression might be effective. Finally, single-copy orthologous genes were applied to construct the phylogenetic relationship of K. punctatus. Results showed that K. punctatus diverged from the common ancestor with Alosa alosa, Alosa pseudoharengus and Sardina pilchardus at approx. 61.16–92.52 MYA. The present study will provide a foundational molecular information for the biological research of K. punctatus.

Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama)

Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of Sillago sinica ∼7.92 Ma. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.