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. 2019 Feb 11;10(2):129.
doi: 10.3390/genes10020129.

Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago (Sillago sihama)

Changxu Tian  1 , Zhiyuan Li  2 , Zhongdian Dong  3 , Yang Huang  4 , Tao Du  5 , Huapu Chen  6 , Dongneng Jiang  7 , Siping Deng  8 , Yulei Zhang  9 , Saetan Wanida  10 , Hongjuan Shi  11 , Tianli Wu  12 , Chunhua Zhu  13 , Guangli Li  14
Affiliations

Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago (Sillago sihama)

Changxu Tian et al. Genes (Basel). .

Abstract

Silver sillago (Sillago sihama) is an emerging commercial marine aquaculture species in China. To date, fundamental information on S. sihama, such as genomic information, is lacking, and no data are available on the gonad transcriptome of S. sihama. Here, the first gonadal transcriptomes of S. sihama have been constructed and genes potentially involved in gonadal development and reproduction identified. Illumina sequencing generated 60.18 million clean reads for the testis and 59.10 million for the ovary. All reads were assembled into 74,038 unigenes with a mean length of 1,004 bp and N50 value of 2,190 bp. Among all the predictable unigenes, a total of 34,104 unigenes (46%) were searched against multiple databases, including 33,244 unigenes annotated in the RefSeq Non- Redundant database at NCBI, and 28,924 in Swiss-Prot. By comparing the ovary and testis, 35,367 unigenes were identified as being differentially expressed between males and females, of which 29,127 were upregulated in the testis and 6,240 were upregulated in the ovary. Numerous differentially expressed genes (DEGs) known to be involved in gonadal development and gametogenesis were identified, including amh, dmrt1, gsdf, cyp19a1a, gnrhr, and zps. Using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, the top 20 KEGG pathways with highest number of DEGs were found to be involved in regulating gonadal development and gametogenesis in S. sihama. Moreover, 22,666 simple sequence repeats (SSRs) were identified in 14,577 SSR-containing sequences. The findings provide a valuable dataset for future functional analyses of sex-associated genes and molecular marker assisted selection in S. sihama.

Keywords: Sillago sihama; differentially expressed genes; gonadal development and gametogenesis; transcriptome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The species distribution of the results of NR annotation. Vertical axes: the number of annotated sequences matching each species. Horizontal axes: the distribution of top species that match the annotated sequences.
Figure 2
Figure 2
Clusters of KOG function classifications of all annotated unigenes in S. sihama gonadal transcriptome. Each function class is represented by a capital letter under the horizontal axis. The vertical axis denotes the number of unigenes in the corresponding function class.
Figure 3
Figure 3
Functional annotation of all unigenes based on GO categorization. The X-axis and Y-axis indicate the GO functions and the number of unigenes with GO function, respectively.
Figure 4
Figure 4
Volcano plot of differences in gene expression between testes and ovaries. Red: upregulated, represents ovary-biased genes; Green: downregulated, represents testis-biased genes.
Figure 5
Figure 5
Distribution of differentially expressed genes (DEGs) among GO terms in biological process, cellular component, and molecular function.
Figure 6
Figure 6
KEGG pathway enrichment analyses of DEGs.
Figure 7
Figure 7
Distribution of identified single sequence repeats (SSRs) according to motif types in the sequences of S. sihama.
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