Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts
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.
KeywordsMacrobrachium rosenbergii BAC Sex chromosome Genome size
This work was supported by the National Key R&D Program of China (project number 2018YFD0900201), the Natural Science Foundation of China (project number 31772841), the Shanghai Sailing Program (project number 17YF1408000), and the Special Fund for the Development of Science and Technology of Shanghai Ocean University (project number A2-0203-17-100201).
Compliance with Ethical Standards
The authors have declared that no competing interest exists.
- Chen S, Zhang G, Shao C, Huang Q, Liu G, Zhang P, Song W, An N, Chalopin D, Volff JN, Hong Y, Li Q, Sha Z, Zhou H, Xie M, Yu Q, Liu Y, Xiang H, Wang N, Wu K, Yang C, Zhou Q, Liao X, Yang L, Hu Q, Zhang J, Meng L, Jin L, Tian Y, Lian J, Yang J, Miao G, Liu S, Liang Z, Yan F, Li Y, Sun B, Zhang H, Zhang J, Zhu Y, Du M, Zhao Y, Schartl M, Tang Q, Wang J (2014) Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nat Genet 46:253–260CrossRefGoogle Scholar
- Gregory TR (2018) Animal genome size database. http://www.genomesize.com. Accessed 15 Sept 2018
- Liu ZJ, Liu SK, Yao J, Bao LS, Zhang JR, Li Y, Jiang C, Sun LY, Wang RJ, Zhang Y, Zhou T, Zeng QF, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun FY, Li C, Wang XZ, Chen A, Jin YL, Yuan ZH, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC (2016b) The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun 7:11757CrossRefGoogle Scholar
- Luo MZ, Wing RA (2003) An improved method for plant BAC library construction. Methods Mol Biol 236:3–20Google Scholar
- Luo MZ, Kim HR, Kudrna D, Sisneros NB, Lee SJ, Mueller C, Collura K, Zuccolo A, Buckingham EB, Grim SM, Yanagiya K, Inoko H, Shiina T, Flajnik MF, Wing RA, Ohta Y (2006) Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics 7:106CrossRefGoogle Scholar
- Soler L, Conte MA, Katagiri T, Howe AE, Lee BY, Amemiya C, Stuart A, Dossat C, Poulain J, Johnson J, Di Palma F, Lindblad-Toh K, Baroiller JF, D'Cotta H, Ozouf-Costaz C, Kocher TD (2010) Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus). BMC Genomics 11:636CrossRefGoogle Scholar
- Wang Y, Lu Y, Zhang Y, Ning Z, Li Y, Zhao Q, Lu H, Huang R, Xia X, Feng Q, Liang X, Liu K, Zhang L, Lu T, Huang T, Fan D, Weng Q, Zhu C, Lu Y, Li W, Wen Z, Zhou C, Tian Q, Kang X, Shi M, Zhang W, Jang S, Du F, He S, Liao L, Li Y, Gui B, He H, Ning Z, Yang C, He L, Luo L, Yang R, Luo Q, Liu X, Li S, Huang W, Xiao L, Lin H, Han B, Zhu Z (2015) The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nat Genet 47:625–631CrossRefGoogle Scholar
- Zhang Y, Zhang X, Scheuring CF, Zhang HB, Huan P, Li F, Xiang J (2008) 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 10:358–365CrossRefGoogle Scholar