Construction Of Cytogenetic Map And Characterization Of Genome In Economically Important Bivalves (Crassostrea Gigas&Chlamys Farreri)

Bivalves, including oysters and scallops, are among the most economically importantclasses in global aquaculture. This study focuses on molecular cytogenetics and genomiccharacterization in economically important species pacific oyster (Crassostrea gigas) andZhikong scallop (Chlamys farreri). It will greatly promote the excavation of gene resources andbreeding.1. Identification of all chromosomes in pacific oyter (Crassostrea gigas)Eighteen bacterial artificial chromosomes (BACs) and18S-28S rDNA gene are mapped onmitotic chromosome spreads in C.gigas with fluorescence in situ hybridization (FISH). Thecombination of probes enables precise identification of all ten chromosome pairs. Based on FISHresults, chromosomes are aligned vertically, and numbered by size.Two out of eighteen BACscan only be unambiguously mapped with the aid of Cot-1DNA. Each BAC is mapped to aunique chromosomal location except one that was mapped on two sites of differentchromosomes.Precise identification and naming system of chromosomes in C.gigas will play animportant role in studies like aneuploidyidentifications and genome instability of polyploidy.Of all mapped BACs, eight were fully sequenced. After Blast search against C.gigasdatabases, approximately50genes are identified including transforming growth factorbetareceptor type-1and metallothionein. Tandem Repeats Finder (TFR) software is used fordiscovery of199microsatellite, one out of which was discovered and has been used for linkageanalysis in previous study. Combining FISH result and linkage information of this marker,linkage group4is assigned to chromosome6. BACs end sequencing of the other10clones generates14high quality sequences. BAC sequences are compared with genome assemblyversion oyster_v9using BlastN.14BACs are anchored in30assembled scaffolds.2. Assignment of pacific oyster (Crassostrea gigas) linkage groups to specific chromosomesAssignment of linkage groups to specific chromosomes as a necessary part of the genomeproject has been carried out in this study for C.gigas. Microsatellite markers are selected from10linkage groups and screened in a BAC library.22BACs that are positive for mappedmicrosatellite markers (including the BAC containing a mapped microsatellite maker mentionedabove) are successfully used for chromosomal assignment with FISH. Referring to chromosomalidentification and naming system developed above,10linkage groups are assigned to10chromosomes respectively. Orientations of8linkage groups are also assigned at the same time.Comparison between linkage groups and chromosome allows examination and revision ofmarker orders and distances.19out of22BACs can only be unambiguously mapped with the aidof Cot-1DNA.19microsatellite sequences are anchored to genome assembly version oyster_v9using BlastN. Microsatellite markers which are anchored in genetic maps, chromosomes andgenome assembly, enable integration of these maps.3. Transcriptome sequencing of Zhikong scallop (Chlamys farreri)Genetic breeding programs have been initiatedfor genetic improvement of scallop species,and research effort has been devoted to identify genes or genetic loci responsible foreconomically important traits such as rapid growth and disease resistance.In this study, denovotranscriptome sequencing is performed by next generation sequencing technology454GSFLX. In a single sequencing run,1,033,636reads were produced and then assembled into26,165contigs.These contigs were then clustered into24,437isotigs and further grouped into20,056isogroups. About47%of the isogroups showed significant matches to known proteinsbased onsequence similarity. Transcripts putatively involved in growth, reproduction andstress/immune-response were identified through Gene ontology (GO) and KEGG pathwayanalyses. Transcriptome comparison with P. yessoensis revealed similar patterns of GOrepresentation. Moreover,38putativefast-evolving genes were identified from1,709orthologousgene pairs between the two scallop species.45,527single nucleotide polymorphisms (SNPs) and 352simple sequence repeats (SSRs) were detected in C. farreri, and20,633SNPs and213SSRswere detected in P. yessoensis.