Genome Structure And Evolutionary Genomic Analysis Of Yesso Scallop

1. Insight into the phylogenomic relationships of ten scallop speciesScallops are a cosmopolitan family, found in all of the world’s oceans. They are amajor grouping of the bivalves which in turn constitute the second largest group ofmollusks. Studies of scallop phylogeny are mainly based on morphological charactersand very limited molecular data so far, and have never come to a genome level.Fortunately, the recent advent of high-throughput sequencing platforms provides theturning point for scallop research, which can dramatically speed up genetic orgenomic studies in potentially any non-model organisms requiring any prior genomeinformation. Here we applied2b-RAD technology, which combined the feture of typeII B enzyme and high-throughput sequencing, to ten scallop species. Theirphylogenetic relationship was constructed using the tag sequences generated by thismethod. The phylogenetic tree was almost consistent with classification based onclassical method. The results also evidenced that the genome of Mimachlamys nobilis,Placopecten magellanicus and Decatopecten plicus were likely to retain morecharacteristics of their ancestor. In addition, species far apart geographically may stillhave a high similarity on their genome feature.2. Transcriptome sequencing and de novo analysis for Yesso ScallopWe performed de novo transcriptome sequencing to first produce a comprehensiveexpressed sequence tag (EST) dataset for the Yesso scallop. In a single454sequencing run,805,330reads were produced and then assembled into32,590contigs,with about six-fold sequencing coverage. A total of25,237unique protein-coding genes were identified from a variety of developmental stages and adult tissues basedon sequence similarities with known proteins. As determined by GO annotation andKEGG pathway mapping, functional annotation of the unigenes recovered diversebiological functions and processes. Transcripts putatively involved in growth,reproduction and stress/immune-response were identified. More than49,000singlenucleotide polymorphisms (SNPs) and2,700simple sequence repeats (SSRs) werealso detected. Comparison of the transcript profiles showed that122unique sequencesfrom different tissues were differentially expressed between the color variant and thecommon scallop. These genes included diverse structural proteins, binding proteinsand regulatory factors. Some genes were putatively involved in the the accumulationand transfer of carotenoids. Others possibly reflected the response of the organism tocarotenoids accumulation. Comparative transcriptome between Yesso scallop andZhikong scallop showed the high similarity between their transcriptome. In addition,148putative fast-evolving genes were adentified in this two species, including betaspectrin, ankyrin and Hsp90. This finding suggested that some upstream regulationfactors may play important roles in the adaptive evolution of scallops. Therelationship between spectrin and ankyrin also implied that during evolution ofscallops, variation in one molecule will possibly trigger the alteration of its closerelated molecules as well.3. Whole genome sequencing and de novo assembly for Yesso scallopThe genome size of Yesso scallop is1.47Gb. Using next-generation sequencingtechnology alone, we have successfully sequenced and de novo assembled a draftsequence of Yesso scallop. Illumina sequencing generated76.7Gb high quality reads,which covered the genome at~52fold. The sequences were assembled into scaffoldswith N50of4,800bp. The total assembly reached to~750Mb. This draft genomecovered90%of the transcriptome sequences, and contained21,300putative gene loci.The total length of genes accounted for16.3%of the whole genome. The number ofexons and intons per gene was4and3, with an average length of1,511bp and3,420bp. Over half of the gene loci obtained annotation informations. Retrotransposons, DNA transposons and simple repeats occupied0.06%,0.01%and0.22%of thegenome, respectively. This study generated comprehensive information about genesand genome structure of Yesso scallop, and provided valuable rescouces for betterunderstanding the the evolutionary and biological complexity of scallops. At the sametime, a fosmid library covering3.3fold of the genome was constructed for Yessoscallop, which was an important part in the whole-genome project. This library willnot only assist the assembly of the genome, construction of physical map and mapsintegration, but also provide recources for map-based gene cloning and its localizationon chromosomes.