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

Tian, Changxu; Li, Zhiyuan; Dong, Zhongdian; Huang, Yang; Du, Tao; Chen, Huapu; Jiang, Dongneng; Deng, Si‐Ping; Zhang, Yulei; Saetan, Wanida; Shi, Hongjuan; Wu, Tian-li; Zhu, Chunhua; Li, Guangli

doi:10.3390/genes10020129

Cited by 37 publications

(34 citation statements)

References 49 publications

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“…Transcription factor SOX-10-like as a member of SRY-related transcription factors from the Sox (Sry-type HMG box) E subfamily was reported to play a critical role in testis development [18,52]. In our research, it was expressed higher in ovaries than that in testes.…”

Section: Discussionsupporting

confidence: 45%

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Jiang

Yuan

Qingqing

et al. 2019

Genes

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The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination. delicious flesh and high value nutrition. Like other crustaceans, M. rosenbergii displays sexual dimorphic growth pattern: The male individuals grow much larger and faster than the females [1,2]. Thus, based on the economic impact, developing the monosex population culture as the efficient approach to boost production has received great attention from researchers in M. rosenbergii. Nevertheless, the premise of monosex culture is to understand the molecular mechanism of sex determination, as well as to unravel sex-related genes.Studies on sex determination have proved that many macruran species exhibit the ZW/ZZ sex determination system [3][4][5]. In M. rosenbergii, sex reversal experiments proposed that the female prawns bear the ZW sex chromosomes, and the male individuals bear the ZZ chromosomes [1,6,7]. Subsequently, isolation of sex-specific markers further deepened the insight of the ZW/ZZ sex determination mode [8,9]. Recently, Ma et al. have confirmed that M. rosenbergii has the ZW/ZZ sex determination system based on the bacterial artificial chromosome (BAC) library, and nine genes were unraveled to be the key sex-linked genes by PacBio sequencing. Amongst, three genes, including zinc knuckle domain (ZKD), reverse transcriptase, and ANCDUO, protein homologs were known genes without characteri...

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Section: Discussionsupporting

confidence: 45%

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Jiang

Yuan

Qingqing

et al. 2019

Genes

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“…To identify genes and biological pathways involved in gonadal development and reproduction, two cDNA libraries from ovaries and testes were prepared and sequenced on the Illumina platform. The N50 length is an important parameter for evaluating assembly quality, and the N50 length of our assembly (3082 bp) was higher than most published transcriptomes of aquatic animals, including Paralichthys olivaceus (809 bp) [9], Patinopecten yessonsis (565 bp) [31], Larimichthys crocea (1,934 bp) [32], Oratosquilla oratoria (1,502 bp) [33], Andrias davidianus (1,557 bp) [17] and Sillago sihama (2,190 bp) [14]. The annotation rate (76.53％ of 62,573) of G. lacustris gonad transcriptomes was higher than the gonad transcriptomes of C. feriatus (37,500, 43.4% of 86,433) [34], S. sihama (34,104 of 74,038) [14] and O. oratoria (19,404 of 37,906) [33].…”

Section: Discussionmentioning

confidence: 87%

“…In addition to master sex determining genes, conserved genes such as cyp19a1a, foxl2, fox3, igf3, sox9, and sf1 are involved in sex determination of fish [9][10][11][12]. Biological pathways, such as the TGF-beta signaling pathway and estrogen signaling pathway, also pay essential roles in sex determination and gonadal development [1, 13,14]. To better understand the regulatory mechanisms underlying sex determination in fish, it is essential to explore genes involved in this process at a broader phylogenetic context.…”

Section: Introductionmentioning

confidence: 99%

“…Transcriptomes allow for general characterization of genes that are expressed in specific tissues or under specific conditions and have been successful in identifying sex-related genes and associated regulatory mechanisms in fish [9,13]. Genes involved in gonad development and gametogenesis have been identified using transcriptomes in many aquatic species, including the channel catfish [15], olive flounder [9,16], Japanese scallop [16], spotted knifejaw [13], Chinese giant salamander (Andrias davidianus) [17] and silver sillago (Sillago sihama) [14] .…”

Section: Introductionmentioning

confidence: 99%

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Comparative transcriptome analysis of the ovary and testis of the lacustrine goby (Gobiopterus lacustris)

Dong

Huang

Zhang

et al. 2019

Preprint

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ABSTRCTLacustrine goby (Gobiopterus lacustris) belongs to a genus of gobies that are small in size and endemic to freshwater, brackish waters or coastal environments around the Indian and Pacific oceans. To date, there are no genomic or transcriptomic studies on G. lacustris. Here, we constructed gonadal transcriptomes of G. lacustris for the first time and identified genes that may be involved in gonadal development and reproduction. In total, 60,657,644 and 52,016,136 clean reads were obtained from ovary and testis, respectively, using Illumina sequencing. Reads were assembled into 62,573 unigenes with N50 value of 3,082 bp and a mean length of 1,869 bp. A total of 47,891 (76.53%) unigenes were annotated in at least one of the seven databases that were used in this study. In addition, 38,550 SSRs (simple sequence repeat, microsatellite) were identified from 20,517 SSR containing sequences. Gene expression patterns in the testis and ovary were compared, and 10,954 DEGs (differentially expressed genes) were identified. Of these genes, 2,383 were up-regulated in the testis and 8,571 were up-regulated in the ovary. RT-qPCR analysis of 14 selected genes showed patterns consistent with the transcriptome results. Numerous DEGs involved in gonadal development and gametogenesis were identified, including foxl2, dmrt1, cyp19a1a, inha, inhb, sycp2, zglp1, tdrp, zps and esra. Using GO and KEGG enrichment analyses, pathways involving regulation of gonadal development and gametogenesis also identified. This work represents the first gonadal transcriptomic analysis of G. lacustris and provides a valuable dataset for future research on the genes involved in reproduction of G. lacustris.

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“…S. sihama is a tropical shallow-water fish species, which is widely distributed in the Indian Ocean and along the coasts of China, Korea, and Japan. It is known as one of the commercially important fish species in East Asia [11,12]. The population of S. sihama has dramatically reduced due to overfishing and environmental pollution [12].…”

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confidence: 99%

Comparative Transcriptome Analysis of Gill Tissue in Response to Hypoxia in Silver Sillago (Sillago sihama)

Saetan

Tian

et al. 2020

Animals

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Simple Summary: Silver sillago (Sillago sihama) is a marine fish species with a high economic value. S. sihama is poorly resistant to hypoxia. However, hypoxia stress-related genes and pathways in S. sihama remain unclear. In this study, we compared gill tissues of S. sihama between hypoxia and normoxia groups and detected differentially expressed genes under hypoxia stress. Two gene families, such as cytochrome P450 and glutathione S-transferase were associated with the function of metabolic process under the hypoxia stress. This study will expand our knowledge about the molecular mechanism of the transcriptome response to hypoxia stress in S. sihama.Abstract: Silver sillago (Sillago sihama) is a commercially important marine fish species in East Asia. In this study, we compared the transcriptome response to hypoxia stress in the gill tissue of S. sihama. The fish were divided into four groups, such as 1 h of hypoxia (hypoxia1h, DO = 1.5 ± 0.1 mg/L), 4 h of hypoxia (hypoxia4h, DO = 1.5 ± 0.1 mg/L), 4 h of reoxygen (reoxygen4h, DO = 8.0 ± 0.2 mg/L) after 4 h of hypoxia (DO = 1.5 mg/L), and normoxia or control (DO = 8.0 ± 0.2 mg/L) groups. Compared to the normoxia group, a total of 3550 genes were identified as differentially expressed genes (DEGs) (log 2 foldchange > 1 and padj < 0.05), including 1103, 1451 and 996 genes in hypoxia1h, hypoxia4h and reoxygen4h groups, respectively. Only 247 DEGs were differentially co-expressed in all treatment groups. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, DEGs were significantly enriched in steroid biosynthesis, biosynthesis of amino acids, glutathione metabolism and metabolism of xenobiotics by cytochrome P450, ferroptosis and drug metabolism-cytochrome P450 pathways. Of these, the cytochrome P450 (CYP) and glutathione S-transferase (GST) gene families were widely expressed. Our study represents the insights into the underlying molecular mechanisms of hypoxia stress.Animals 2020, 10, 628 2 of 13 the aquatic environment, which can be accelerated by several factors, such as human activities, water pollution, and intensive fish farming [1]. To adapt to the hypoxic environment, fish produce a range of adaptive physiological mechanisms, such as a rapid change in cell metabolism using ATP [2], regulation of respiratory function [3], floating head [4], and neurological, immune, and hormonal responses [5]. Severe hypoxia can even affect fish reproduction, survival, and cell metabolism [6]. The fish gill is the primary organ for physiological exchanges with the surrounding environment [7]. The fish gill plays a dominant role in aquatic gas exchange and is capable of extensive remodeling in response to changes in the DO level [8]. Many fish respond to hypoxia by increasing the functional surface area of their gill [4]. When the fish returns to normoxic water, the hypoxia-induced gill remodeling is reversed due to the embedding of gill lamellae [9].The sillago silver (Sillago sihama) is a popular species of the family Sillaginidae [10]. S. sihama is ...

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

Cited by 37 publications

References 49 publications

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Comparative transcriptome analysis of the ovary and testis of the lacustrine goby (Gobiopterus lacustris)

Comparative Transcriptome Analysis of Gill Tissue in Response to Hypoxia in Silver Sillago (Sillago sihama)

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