Zhikong scallop (Chlamys farreri Jones et Preston) is one of the most economically important aquaculture species in China, and its production has reached approximately 80% of the total scallop production. However, the frequent mass mortality of the species has seriously affected the development of its industry since 1996. To develop new scallop genotypes to manage the problem, it is necessary to have a better understanding of the molecular mechanisms underlying its economically quantitative and qualitative traits, such as disease resistance and growth rate. Therefore, many investigations have recently focused on genome research of the species.
In support of the Key Program of National Natural Science Foundation of China “BAC-based physical mapping and integrated with genetic map in Zhikong scallop (Chlamys farreri)”, a research team, led by Prof. Jianghai Xiang at Institute of Oceanology, Chinese Academy of Sciences, had developed a genome-wide, BAC-based physical map for the species. A total of 81,408 clones from two bacterial artificial chromosome (BAC) libraries of the scallop were fingerprinted using an ABI 3130xl Genetic Analyzer and a fingerprinting kit developed in their laboratory. After data processing, 63,641 (~5.8 × genome coverage) fingerprints were validated and used in the physical map assembly. A total of 3,696 contigs were assembled for the physical map. Each contig contained an average of 10.0 clones, with an average physical size of 490 kb. The combined total physical size of all contigs was 1.81 Gb, equivalent to approximately 1.5 fold of the scallop haploid genome. A total of 10,587 BAC end sequences (BESs) and 167 markers were mapped into the physical map. A initial integration of the physical map with a microsatellite genetic map was tried. They evaluated the physical map by overgo hybridization, BAC-FISH (fluorescence in situ hybridization), contig BAC pool screening and source BAC library screening. The results have provided evidence of the high reliability of the contig physical map.
Physical maps are crucial tools for genome sequencing, gene mapping and cloning, genetic improvement and selective breeding. Although the development of whole-genome shotgun sequence draft maps based on Next-generation sequencing (NGS) has become cost-effective recently, a physical map remains an important component of genome sequencing projects. For the large regions of repeat sequences and highly heterozygous genomes, sequencing and assembly will not be easily addressed by NGS alone. Additional tools are needed to provide anchor points to link sequence contigs and bridge the large repeat regions. Physical maps, specially the contig physical maps constructed based on restriction fragment fingerprints of BAC clones, can provide these anchor points for genome sequence assembling. Moreover, genome-wide integrative physical and genetic mapping is a most efficient and economical approach to fine mapping and positional cloning of genes controlling many phenotypic traits such as quantitative trait loci (QTLs).
This is the first physical map in mollusc in the world and the first physical map of marine aquaculture animal in China. It will provide an important platform for advanced research of genomics and genetics, and mapping of genes and QTLs of economical importance, thus facilitating the genetic improvement and selective breeding of the scallop and other marine molluscs.
The paper was recently published in PLoS ONE and is available online at http://dx.plos.org/10.1371/journal.pone.0027612.