Transcriptome Using Illumina Sequencing Reveals the Traits of Spermatogenesis and Developing Testes in Eriocheir Sinensis

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2017 Feb 18

PMID 28212420

Citations 12

Authors

Gen-Liang Li

Hui Qian

Affiliations

Soon will be listed here.

Abstract

Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145.19 M clean reads representing with a total of 21.34 Gb bases and 45.48% GC content. 56.30% clean reads were mapped to the draft genome of E. sinensis. The assembly of the transcriptome yielded contigs of 5691802 sequences and unigenes of 406527 sequences. Total 24246 and 40793 transcripts were annotated using Swissprot and Nr database, respectively. There were 48213 (70.31%) and 7858 (46.25%) transcripts with identity of more than 99 matching to mature testis unigenes in the databases of Nr and EST, respectively. The analytic results of KOG, GO and KEGG showed wide potential molecular functions of transcripts in the developing testes. KEGG analysis of unigenes yielded total 9422 predicted genes. Those predicted genes were involved in total 216 KEGG pathways related to the physiological activities of developing testis. 1975 predicted genes were involved in cellular and subcellular structural alteration of male germ cells. There were important roles of some pathways in the processes of morphological and structural biogenesis pertaining to testis development and spermatogenesis. Other 583 unigenes encoding the genetic and epigenetic factors also be found, which might contribute to the decondensation and stability of decondensed nuclei in the spermatozoa. These predicted events provide a view of the potential molecular mechanisms of development of testis and spermatogenesis in E. sinensis.

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References

Hou C, Yang W . Characterization and expression pattern of p53 during spermatogenesis in the Chinese mitten crab Eriocheir sinensis. Mol Biol Rep. 2012; 40(2):1043-51. DOI: 10.1007/s11033-012-2145-3. View

Nusse O . Biochemistry of the phagosome: the challenge to study a transient organelle. ScientificWorldJournal. 2011; 11:2364-81. PMC: 3236389. DOI: 10.1100/2011/741046. View

Nagano M, Yeh J . The identity and fate decision control of spermatogonial stem cells: where is the point of no return?. Curr Top Dev Biol. 2013; 102:61-95. DOI: 10.1016/B978-0-12-416024-8.00003-9. View

Pesin J, Orr-Weaver T . Regulation of APC/C activators in mitosis and meiosis. Annu Rev Cell Dev Biol. 2008; 24:475-99. PMC: 4070676. DOI: 10.1146/annurev.cellbio.041408.115949. View

Bonifacino J, Traub L . Signals for sorting of transmembrane proteins to endosomes and lysosomes. Annu Rev Biochem. 2003; 72:395-447. DOI: 10.1146/annurev.biochem.72.121801.161800. View

Kumar A, Mocklinghoff S, Yumoto F, Jaroszewski L, Farr C, Grzechnik A . Structure of a novel winged-helix like domain from human NFRKB protein. PLoS One. 2012; 7(9):e43761. PMC: 3439487. DOI: 10.1371/journal.pone.0043761. View

Kimura H, Tsuboi D, Wang C, Kushima I, Koide T, Ikeda M . Identification of Rare, Single-Nucleotide Mutations in NDE1 and Their Contributions to Schizophrenia Susceptibility. Schizophr Bull. 2014; 41(3):744-53. PMC: 4393687. DOI: 10.1093/schbul/sbu147. View

Komeya M, Ogawa T . Spermatogonial stem cells: Progress and prospects. Asian J Androl. 2015; 17(5):771-5. PMC: 4577589. DOI: 10.4103/1008-682X.154995. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

10.

Song L, Bian C, Luo Y, Wang L, You X, Li J . Draft genome of the Chinese mitten crab, Eriocheir sinensis. Gigascience. 2016; 5:5. PMC: 4730596. DOI: 10.1186/s13742-016-0112-y. View

11.

Li G, Kang X, Mu S, Guo M, Huang S, Chen Q . H3K9ac involved in the decondensation of spermatozoal nuclei during spermatogenesis in Chinese mitten crab Eriocheir sinensis. Cytotechnology. 2016; 69(1):75-87. PMC: 5264624. DOI: 10.1007/s10616-016-0038-3. View

12.

Kron S, Gow N . Budding yeast morphogenesis: signalling, cytoskeleton and cell cycle. Curr Opin Cell Biol. 1995; 7(6):845-55. DOI: 10.1016/0955-0674(95)80069-7. View

13.

Demidova A, Aau M, Zhuang L, Yu Q . Dual regulation of Cdc25A by Chk1 and p53-ATF3 in DNA replication checkpoint control. J Biol Chem. 2008; 284(7):4132-9. DOI: 10.1074/jbc.M808118200. View

14.

Lu Y, Wang Q, Wang D, Zhou H, Hu Y, Yang W . Functional Analysis of KIF3A and KIF3B during Spermiogenesis of Chinese Mitten Crab Eriocheir sinensis. PLoS One. 2014; 9(5):e97645. PMC: 4037190. DOI: 10.1371/journal.pone.0097645. View

15.

Cooke P, Simon L, Nanjappa M, Medrano T, Berry S . Plasticity of spermatogonial stem cells. Asian J Androl. 2015; 17(3):355-9. PMC: 4430932. DOI: 10.4103/1008-682X.148072. View

16.

Zhang W, Wan H, Jiang H, Zhao Y, Zhang X, Hu S . A transcriptome analysis of mitten crab testes (Eriocheir sinensis). Genet Mol Biol. 2011; 34(1):136-41. PMC: 3085360. DOI: 10.1590/S1415-47572010005000099. View

17.

Mazzolini L, Broban A, Froment C, Burlet-Schiltz O, Besson A, Manenti S . Phosphorylation of CDC25A on SER283 in late S/G2 by CDK/cyclin complexes accelerates mitotic entry. Cell Cycle. 2016; 15(20):2742-52. PMC: 5053558. DOI: 10.1080/15384101.2016.1220455. View

18.

Zhang Z, Mu S, Guo M, Wu J, Li Y, Zhang H . Dynamics of histone H2A, H4 and HS1ph during spermatogenesis with a focus on chromatin condensation and maturity of spermatozoa. Sci Rep. 2016; 6:25089. PMC: 4848542. DOI: 10.1038/srep25089. View

19.

Mendenhall M, Hodge A . Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1998; 62(4):1191-243. PMC: 98944. DOI: 10.1128/MMBR.62.4.1191-1243.1998. View

20.

Lee G, Kim J, Taylor M, Muller M . DNA methyltransferase 1-associated protein (DMAP1) is a co-repressor that stimulates DNA methylation globally and locally at sites of double strand break repair. J Biol Chem. 2010; 285(48):37630-40. PMC: 2988368. DOI: 10.1074/jbc.M110.148536. View