Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium Rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts

Overview

Journal Mar Biotechnol (NY)

Specialties Biology
Biotechnology

Date 2019 Jan 12

PMID 30632018

Citations 5

Authors

Ke-Yi Ma

Shu-Hui Yu

Yu-Xin Du

Shi-Qing Feng

Liang-Jie Qiu

Dai-Yi Ke

Mei-Zhong Luo

Gao-Feng Qiu

Affiliations

Soon will be listed here.

Abstract

Knowledge on sex determination has proven valuable for commercial production of the prawn Macrobrachium rosenbergii due to sex dimorphism of the male and female individuals. Previous studies indicated that prawn sex is determined by a ZW-ZZ chromosomal system, but no genomic information is available for the sex chromosome. Herein, we constructed a genomic bacterial artificial chromosome (BAC) library and identified the ZW-derived BAC clones for initial analysis of the sex chromosomal DNA sequence. The arrayed BAC library contains 200,448 clones with average insert size of 115.4 kb, corresponding to ∼ 4× coverage of the estimated 5.38 Gb genome. Based on a short female-specific marker, a Z- and a W-fragment were retrieved with the genomic walking method. Screening the BAC library using a ZW-specific marker as probe resulted in 12 positive clones. From these, a Z-derived (P331M17) and a W-derived (P122G2) BAC clones were randomly selected and sequenced by PacBio method. We report the construction of a large insert, deep-coverage, and high-quality BAC library for M. rosenbergii that provides a useful resource for positional cloning of target genes, genomic organization, and comparative genomics analysis. Our study not only confirmed the ZW/ZZ system but also discovered sex-linked genes on ZW chromosomes for the first time, contributing to a comprehensive understanding of the genomic structure of sex chromosomes in M. rosenbergii.

Citing Articles

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References

Luo M, Wang Y, Frisch D, Joobeur T, Wing R, Dean R . Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome. 2001; 44(2):154-62. View

Gong S, Yang X, Li C, Heintz N . Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kgamma origin of replication. Genome Res. 2002; 12(12):1992-8. PMC: 187570. DOI: 10.1101/gr.476202. View

Dolezel J, Bartos J, Voglmayr H, Greilhuber J . Nuclear DNA content and genome size of trout and human. Cytometry A. 2003; 51(2):127-8; author reply 129. DOI: 10.1002/cyto.a.10013. View

Botstein D, Risch N . Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet. 2003; 33 Suppl:228-37. DOI: 10.1038/ng1090. View

Tremblay J, Viger R . A mutated form of steroidogenic factor 1 (SF-1 G35E) that causes sex reversal in humans fails to synergize with transcription factor GATA-4. J Biol Chem. 2003; 278(43):42637-42. DOI: 10.1074/jbc.M305485200. View

Zarkower D, Hodgkin J . Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding two zinc finger proteins. Cell. 1992; 70(2):237-49. DOI: 10.1016/0092-8674(92)90099-x. View

Luo M, Wing R . An improved method for plant BAC library construction. Methods Mol Biol. 2003; 236:3-20. DOI: 10.1385/1-59259-413-1:3. View

Katagiri T, Asakawa S, Hirono I, Aoki T, Shimizu N . Genomic bacterial artificial chromosome library of the Japanese flounder Paralichthys olivaceus. Mar Biotechnol (NY). 2004; 2(6):571-6. DOI: 10.1007/s101260000041. View

Darling A, Mau B, Blattner F, Perna N . Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004; 14(7):1394-403. PMC: 442156. DOI: 10.1101/gr.2289704. View

10.

Charlesworth D, Charlesworth B, Marais G . Steps in the evolution of heteromorphic sex chromosomes. Heredity (Edinb). 2005; 95(2):118-28. DOI: 10.1038/sj.hdy.6800697. View

11.

Stanke M, Morgenstern B . AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005; 33(Web Server issue):W465-7. PMC: 1160219. DOI: 10.1093/nar/gki458. View

12.

Luo M, Kim H, Kudrna D, Sisneros N, Lee S, Mueller C . Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics. 2006; 7:106. PMC: 1513397. DOI: 10.1186/1471-2164-7-106. View

13.

Xu P, Wang S, Liu L, Peatman E, Somridhivej B, Thimmapuram J . Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species. Anim Genet. 2006; 37(4):321-6. DOI: 10.1111/j.1365-2052.2006.01453.x. View

14.

Zhang L, Yang C, Zhang Y, Li L, Zhang X, Zhang Q . A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica. 2006; 131(1):37-49. DOI: 10.1007/s10709-006-9111-8. View

15.

Rees D, Dufresne F, Glemet H, Belzile C . Amphipod genome sizes: first estimates for Arctic species reveal genomic giants. Genome. 2007; 50(2):151-8. DOI: 10.1139/g06-155. View

16.

Zhang Y, Zhang X, Scheuring C, Zhang H, Huan P, Li F . Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system. Mar Biotechnol (NY). 2008; 10(4):358-65. DOI: 10.1007/s10126-007-9071-8. View

17.

Ford A . Can you feminise a crustacean?. Aquat Toxicol. 2008; 88(4):316-21. DOI: 10.1016/j.aquatox.2008.04.013. View

18.

Staelens J, Rombaut D, Vercauteren I, Argue B, Benzie J, Vuylsteke M . High-density linkage maps and sex-linked markers for the black tiger shrimp (Penaeus monodon). Genetics. 2008; 179(2):917-25. PMC: 2429885. DOI: 10.1534/genetics.107.080150. View

19.

Ventura T, Manor R, Aflalo E, Weil S, Raviv S, Glazer L . Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis. Endocrinology. 2008; 150(3):1278-86. DOI: 10.1210/en.2008-0906. View

20.

Zhang X, Zhang Y, Scheuring C, Zhang H, Huan P, Wang B . Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei. Mar Biotechnol (NY). 2009; 12(2):141-9. DOI: 10.1007/s10126-009-9209-y. View