De Novo Transcriptome Analysis of the Lizard Fish (Saurida elongata): Novel Insights into Genes Related to Sex Differentiation
Source abstract
Abstract
Among vertebrates, teleost fishes exhibit the largest array of sex-determining systems, resulting in many reproductive strategies. Screening these fish for sex-related genes could enhance our understanding of sexual differentiation. The lizardfish, Saurida elongata (Temminck & Schlegel, 1846), is a commercially important marine fish in tropical and subtropical seas of the northwest Pacific. However, little genomic information on S. elongata is available. In this study, the transcriptomes of three female and three male S. elongata were sequenced. A total of 49.19 million raw read pairs were generated. After identification and assembly, a total of 59,902 nonredundant unigenes were obtained with an N50 length of 2070 bp. Then, 38,016 unigenes (63.47% of the total) were successfully annotated through multiple public databases. A comparison of the unigenes of different sexes of S. elongata revealed that 22,507 unigenes (10,419 up-regulated in a female and 12,088 up-regulated in a male) were differentially expressed between sexes. Then, numerous candidate sex-related genes were identified, including dmrt2, dmrt4, foxl2, zps and starts. Furthermore, 23,941 simple sequence repeats (SSRs) were detected in SSR-containing sequences. This informative transcriptome analysis provides valuable data to increase the genomic resources of S. elongata.
Source: crossref · Quality: baseline
Research context
OpenAlex topics: Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities · Reproductive biology and impacts on aquatic species · Genetic diversity and population structure
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Key Laboratory of Marine Ranching, Ministry of Agriculture Rural Affairs, Guangzhou 510300, China
Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China
Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangzhou 510300, China
Shenzhen Fisheries Development Research Center, Shenzhen 518067, China
Funding
Asia Cooperation Fund Project—Modern fishery cooperation between China and neighboring countries around the South China Sea
References (65)
Show source-provided references
1. Loss of Wnt4 and Foxl2 leads to female-to-male sex reversal extending to germ cells10.1093/hmg/ddm235 ↗
2. The avian Z-linked gene DMRT1 is required for male sex determination in the chicken10.1038/nature08298 ↗
3. Lavery, R., Chassot, A.A., Pauper, E., Gregoire, E.P., Klopfenstein, M., de Rooij, D.G., Mark, M., Schedl, A., Ghyselinck, N.B., and Chaboissier, M.C. (2012). Testicular differentiation occurs in absence of R-spondin1 and Sox9 in mouse sex reversals. PLoS Genet., 8.10.1371/journal.pgen.1003170 ↗
4. The decapod researcher’s guide to the galaxy of sex determination10.1007/s10750-017-3452-4 ↗
5. Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis10.1186/s12864-018-4756-0 ↗
6. Blurring the edges in vertebrate sex determination10.1016/j.gde.2008.11.004 ↗
7. Vertebrate sex-determining genes play musical chairs10.1016/j.crvi.2016.05.010 ↗
8. Diversity and plasticity of sex determination and differentiation in fishes10.1159/000342009 ↗
9. Sex Change in Clownfish: Molecular insights from transcriptome analysis10.1038/srep35461 ↗
10. Sexual growth dimorphism in sea bass Dicentrarchus labrax10.1016/S0044-8486(01)00786-4 ↗
11. Analysis of sexually dimorphic growth in captive reared cobia (Rachycentron canadum) and the occurrence of intersex individuals10.1016/j.aquaculture.2016.09.044 ↗
12. Transcriptomics analysis revealing candidate networks and genes for the body size sexual dimorphism of Chinese tongue sole (Cynoglossus semilaevis)10.1007/s10142-018-0595-y ↗
13. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar10.1186/s12864-017-3652-3 ↗
14. Age and growth of the lizardfish Saurida sp. 1 in the East China Sea using otolith ring marks10.1016/S0165-7836(01)00285-5 ↗
15. Age and growth of the lizardfish Saurida elongata from the Tsushima/Korea Strait10.1007/s12562-009-0108-y ↗
16. Agriculture Effects of maturation and spawning on the gel-forming ability of lizardfish (Saurida elongata) muscle tissues10.1002/jsfa.2740520306 ↗
17. Optimization of hydrolysis conditions for the production of angiotensin-I converting enzyme-inhibitory peptides and isolation of a novel peptide from lizard fish (Saurida elongata) muscle protein hydrolysate10.3390/md10051066 ↗
18. Studies on the interaction between angiotensin-converting enzyme (ACE) and ACE inhibitory peptide from Saurida elongata10.1021/acs.jafc.8b04303 ↗
19. Distribution of relative abundance of slender lizardfish and its influencing factors in southern coastal waters of Shandong during autumn
20. The low mitochondrial diversities in lizardfish Saurida elongata: Recent population expansion and selection10.1016/j.bse.2016.06.011 ↗
21. Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity10.1016/j.ygeno.2020.01.022 ↗
22. De novo transcriptome characterization and growth-related gene expression profiling of diploid and triploid bighead catfish (Clarias macrocephalus Gunther, 1864)10.1007/s10126-017-9730-3 ↗
23. Transcriptome analysis for identification of candidate genes related to sex determination and growth in Charybdis japonica10.1016/j.gene.2018.07.044 ↗
24. Ma, D., Ma, A., Huang, Z., Wang, G.N., Wang, T., Xia, D., and Ma, B. (2016). Transcriptome analysis for identification of genes related to gonad differentiation, growth, immune response and marker discovery in the turbot (Scophthalmus maximus). PLoS ONE, 11.10.1371/journal.pone.0149414 ↗
25. Tian, C., Li, Z., Dong, Z., Huang, Y., Du, T., Chen, H., Jiang, D., Deng, S., Zhang, Y., and Wandia, S. (2019). Transcriptome analysis of male and female mature gonads of silver sillago (Sillago sihama). Genes, 10.10.3390/genes10020129 ↗
26. Comparative transcriptomic analysis for identification of candidate sex-related genes and pathways in Crimson seabream (Parargyrops edita)10.1038/s41598-020-80282-5 ↗
27. The RIN: An RNA integrity number for assigning integrity values to RNA measurements10.1186/1471-2199-7-3 ↗
28. Trimmomatic: A flexible trimmer for Illumina sequence data10.1093/bioinformatics/btu170 ↗
29. Trinity: Reconstructing a full-length transcriptome without a genome from RNA-Seq data10.1038/nbt.1883 ↗
30. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs10.1093/bioinformatics/btv351 ↗
31. Fast gapped-read alignment with Bowtie 210.1038/nmeth.1923 ↗
32. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome10.1186/1471-2105-12-323 ↗
33. DEGseq: An R package for identifying differentially expressed genes from RNA-seq data10.1093/bioinformatics/btp612 ↗
34. Primer3—New capabilities and interfaces10.1093/nar/gks596 ↗
35. Appropriate ’housekeeping’ genes for use in expression profiling the effects of environmental estrogens in fish10.1186/1471-2199-8-10 ↗
36. Novel galanin receptors in teleost fish: Identification, expression and regulation by sex steroids10.1016/j.ygcen.2014.06.030 ↗
37. Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi, Lates calcarifer10.1111/age.12312 ↗
38. annot8r: GO, EC and KEGG annotation of EST datasets10.1186/1471-2105-9-180 ↗
39. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences10.1016/j.jmb.2015.11.006 ↗
40. Rozenfeld, C., Blanca, J., Gallego, V., García-Carpintero, V., Herranz-Jusdado, J., Pérez, L., Asturiano, J.F., Cañizares, J., and Peñaranda, D.S. (2019). De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages. PLoS ONE, 14.10.1371/journal.pone.0218085 ↗
41. The biology and chemistry of fertilization10.1126/science.3027891 ↗
42. Molecular analysis of cDNA coding for ZP3, a sperm binding protein of the mouse zona pellucida10.1016/0012-1606(88)90315-6 ↗
43. Dumont, J.N., and Brummett, A.R.J.O. (1985). Egg Envelopes in Vertebrates. Oogenesis, Springer.10.1007/978-1-4615-6814-8_5 ↗
44. Egg extracellular coat proteins: From fish to mammals
45. Study on the zona pellucida 4 (ZP4) gene sequence and its expression in the ovaries of patients with polycystic ovary syndrome10.1007/s40618-015-0260-4 ↗
46. Novel sex-determining genes in fish and sex chromosome evolution10.1002/dvdy.23927 ↗
47. Isolation of doublesex- and mab-3-related transcription factor 6 and its involvement in spermatogenesis in tilapia10.1095/biolreprod.114.121418 ↗
48. The mammalian doublesex homolog DMRT1 is a transcriptional gatekeeper that controls the mitosis versus meiosis decision in male germ cells10.1016/j.devcel.2010.09.010 ↗
49. The Drosophila doublesex proteins share a novel zinc finger related DNA binding domain10.1002/j.1460-2075.1993.tb05684.x ↗
50. DMRT1 promotes oogenesis by transcriptional activation of Stra8 in the mammalian fetal ovary10.1016/j.ydbio.2011.05.658 ↗
51. Male-biased expression of X-chromosomal DM domain-less Dmrt8 genes in the mouse10.1016/j.ygeno.2006.01.003 ↗
52. Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (Oreochromis niloticus)10.1016/j.btre.2019.e00398 ↗
53. Sex dimorphic expression of five dmrt genes identified in the Atlantic cod genome. The fish-specific dmrt2b diverged from dmrt2a before the fish whole-genome duplication10.1016/j.gene.2012.06.021 ↗
54. Fish specific duplication of Dmrt2: Characterization of zebrafish Dmrt2b10.1016/j.biochi.2008.02.021 ↗
55. Expression of the DMRT gene and its roles in early gonadal development of the Japanese pufferfish Takifugu rubripes
56. Expression analysis and characterization of dmrt2 in Chinese tongue sole (Cynoglossus semilaevis)10.1016/j.theriogenology.2019.06.035 ↗
57. Lourenco, R., Lopes, S.S., and Saude, L. (2010). Left-right function of dmrt2 genes is not conserved between zebrafish and mouse. PLoS ONE, 5.10.1371/journal.pone.0014438 ↗
58. Zebrafish Dmrta2 regulates neurogenesis in the telencephalon10.1111/j.1365-2443.2011.01555.x ↗
59. Sexually dimorphic expression of two types of DM (Doublesex/Mab-3)-domain genes in a teleost fish, the Tilapia (Oreochromis niloticus)10.1006/bbrc.2000.2840 ↗
60. Molecular cloning and sexually dimorphic expression of DMRT4 gene in Oreochromis aureus10.1007/s11033-009-9820-z ↗
61. Expression pattern of dmrt4 from olive flounder (Paralichthys olivaceus) in adult gonads and during embryogenesis10.1007/s10695-008-9267-5 ↗
62. Molecular cloning and analysis of gonadal expression of Foxl2 in the medaka, Oryzias latipes10.1016/j.bbrc.2006.03.137 ↗
63. Roles of forkhead box protein L2 (foxl2) during gonad differentiation and maintenance in a fish, the olive flounder (Paralichthys olivaceus)10.1071/RD18233 ↗
64. Differential expression analysis of genes involved in high-temperature induced sex differentiation in Nile tilapia10.1016/j.cbpb.2014.08.006 ↗
65. Blockage of androgen and administration of estrogen induce transdifferentiation of testis into ovary10.1530/JOE-16-0551 ↗