Abstract
The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33 %. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.
Similar content being viewed by others
References
An HS, Lee JW, Hong SW (2013) Population genetic structure of the Korean Pacific abalone Haliotis diversicolor supertexta inferred from microsatellite marker analysis. Biochem Syst Ecol 48:76–84. doi:10.1016/j.bse.2012.11.010
Arrach N, Hernandez J, Hussein T (2014) Detection of sex chromosome abnormalities: array CGH vs next generation sequencing. Fertil Steril 102:e183
Cheng W, Hsiao I-S, Chen J-C (2004) Effect of ammonia on the immune response of Taiwan abalone Haliotis diversicolor supertexta and its susceptibility to Vibrio parahaemolyticus. Fish Shellfish Immunol 17:193–202
Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485
Cunningham C, Hikima J-I, Jenny MJ, Chapman RW, Fang G-C, Saski C, Lundqvist ML, Wing RA, Cupit PM, Gross PS (2006) New resources for marine genomics: bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas). Mar Biotechnol 8:521–533
Eierman LE, Hare MP (2014) Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica. BMC Genomics 15:503
Geiger DL (1999) Distribution and biogeography of the recent Haliotidae (Gastropoda: Vetigastropoda) world-wide. Boll Malacol 35:57–120
Jang S, Liu H, Su J, Dong F, Xiong F, Liao L, Wang Y, Zhu Z (2010) Construction and characterization of two bacterial artificial chromosome libraries of grass carp. Mar Biotechnol 12:261–266
Ji P, Liu G, Xu J, Wang X, Li J, Zhao Z, Zhang X, Zhang Y, Xu P, Sun X (2012) Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS One 7:e35152
Jiang J-Z, Zhang W, Guo Z-X, Cai C-C, Su Y-L, Wang R-X, Wang J-Y (2011) Functional annotation of an expressed sequence tag library from Haliotis diversicolor and analysis of its plant-like sequences. Mar Genomics 4:189–196
Li S, Chou H-H (2004) LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20:2865–2866
Li D, Kang D, Yin Q, Sun X, Liang L (2007) Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinus carpio L.) populations. J Genet Genomics 34:984–993
Li Q, Shu J, Zhao C, Liu S, Kong L, Zheng X (2010) Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai). Chin J Oceanol Limnol 28:46–54
Li Y, Xu P, Zhao Z, Wang J, Zhang Y, Sun X-W (2011) Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio. Mar Biotechnol 13:706–712
Lindberg DR, Shepherd SA, Tegner MJ, del Próo Gutzmán SA (1992) Evolution, distribution and systematics of Haliotidae. In: Shepherd SA, Tegner MJ, Gutzmánd del Próo SA (eds) Abalone of the world: biology, fisheries and culture. Blackwell Scientific Publishing, London, pp 3–18
Liu J, Zeng B, Du T, Rao Y (2013) Low genetic diversity and genetic differentiation among domesticated stocks of the small abalone Haliotis diversicolor in China. Afr J Biotechnol 10:19267–19275
Palti Y, Luo M-C, Hu Y, Genet C, You FM, Vallejo RL, Thorgaard GH, Wheeler PA, Rexroad CE (2009) A first generation BAC-based physical map of the rainbow trout genome. BMC Genomics 10:462
Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S (2013) Reprint of: evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet 7:632–639
Sambrook J, Russell DW, Russell DW (2006) The condensed protocols from molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Sekino M, Hara M (2007) Linkage maps for the Pacific abalone (genus Haliotis) based on microsatellite DNA markers. Genetics 175:945–958
Shi Y, Guo X, Gu Z, Wang A, Wang Y (2010) Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve. Chin J Oceanol Limnol 28:549–557
Somridhivej B, Wang S, Sha Z, Liu H, Quilang J, Xu P, Li P, Hu Z, Liu Z (2008) Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of channel catfish (Ictalurus punctatus): a resource for integration of linkage and physical maps. Aquaculture 275:76–80
Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, Shoguchi E, Fujiwara M, Shinzato C, Hisata K (2012) Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res 19:117–130
Thorsen J, Zhu B, Frengen E, Osoegawa K, De Jong PJ, Koop BF, Davidson WS, Høyheim B (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics 6:50
Wang S, Xu P, Thorsen J, Zhu B, De Jong PJ, Waldbieser G, Kucuktas H, Liu Z (2007) Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. Mar Biotechnol 9:701–711
Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z (2007) A BAC-based physical map of the channel catfish genome. Genomics 90:380–388
Xu P, Wang J, Wang J, Cui R, Li Y, Zhao Z, Ji P, Zhang Y, Li J, Sun X (2011) Generation of the first BAC-based physical map of the common carp genome. BMC Genomics 12:537
You WW, Ke CH, Luo X, Wang DX (2009) Growth and survival of three small abalone Haliotis diversicolor populations and their reciprocal crosses. Aquac Res 40:1474–1480
Zhan X, Fan F, You W, Yu J, Ke C (2012) Construction of an integrated map of Haliotis diversicolor using microsatellite markers. Mar Biotechnol 14:79–86
Zhang Y, Liang L, Jiang P, Li D, Lu C, Sun X (2008a) Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family. J Genet Genomics 35:97–103
Zhang Y, Zhang X, Scheuring CF, Zhang H-B, Huan P, Li F, Xiang J (2008b) 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 10:358–365
Zhang X, Zhang Y, Scheuring C, Zhang H-B, Huan P, Wang B, Liu C, Li F, Liu B, Xiang J (2010) Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei. Mar Biotechnol 12:141–149
Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, Cao D, Li C, Chang Y, Hou N, Li H (2011) Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp (Cyprinus carpio L.). Mar Biotechnol 13:376–392
Zhou J, Wu Q, Wang Z, Ye Y (2004) Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Russ J Genet 40:1144–1148
Acknowledgments
We acknowledge grant support from National Natural Science Foundation of China (No. U1205121 and 31422057), the National High-Technology Research and Development Program of China (863 program; 2011AA100401), Special Scientific Research Funds for Central Non-profit Institutes of Chinese Academy of Fishery Sciences (2013A03YQ01). The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding this research (No. RG 1435–012).
Conflict of Interest
The authors declare that they have no competing interests.
Authors’ Contributions
PX and CK conceived the study. LJ worked on BAC library evaluation, BAC pooling, BAC screening, BAC sequencing, assembly, and manuscript drafting. WY worked on sample preparation and collection and participated in the manuscript preparation. XZ and KW worked on agar plugs preparation for HMW genomic DNA extraction. ZZ, KW, and BC worked on BAC pooling and screening. JX and YJ worked on BAC sequencing and sequencing analysis. PX wrote the manuscript. YZ, SM, and KAG helped on the manuscript revision. All authors read and approved the final manuscript.
Author information
Authors and Affiliations
Corresponding authors
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
Supplemental Table S1
(DOCX 21 kb)
Supplemental Table S2
(DOCX 34 kb)
Rights and permissions
About this article
Cite this article
Jiang, L., You, W., Zhang, X. et al. Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization. Mar Biotechnol 18, 49–56 (2016). https://doi.org/10.1007/s10126-015-9666-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-015-9666-4