摘要:草蝦是全世界最重要的養殖蝦種,然而近年來草蝦產業飽受疫病侵襲,野生母族群數量亦有逐漸枯竭之虞。草蝦雖富經濟價值,然而學界於蝦體生長、生殖、免疫調控等方面累積之基礎生物學極少,對其基因體之瞭解更是有限。因此,本計畫擬以瞭解草蝦基因體為目標,由草蝦fosmid基因體庫(五倍涵覆率)中,篩選對蝦體生存或生殖過程中具重要影響之基因—尤其是與蝦體抗病、抗緊迫、及性別分化相關者。此外,為瞭解草蝦之基因體,我們將採取「浮掠定序」的策略,基因體定序之範圍限於含標的基因之部分基因體區域。基因體序列建立初稿之後,我們將定序來自不同族群的個體(包括台灣、菲律賓、越南、澳洲、泰國東部、泰國西部、馬達加斯加等族群),以瞭解這些基因體區域在族群間之遺傳變異、並建立單核苷酸多型性(SNPs)圖譜。SNPs圖譜將有助於鑑別基因體中受正或負向選汰的重要基因。經序列分析後,若發現某對偶基因之頻度過高(或過低)、遺傳歧異度過高(或過低)、族群分化度增加、或過強的聯鎖不平衡等現象時,即可推知此基因體區域曾受過選汰的影響。這些知識將有助於解決草蝦養殖產業中所遭遇之疫病問題,並期能有效地改善草蝦養殖之產能。
Abstract: Abstract
The black tiger shrimp, Penaeus monodon, is the most important shrimp aquaculture species in the world especially in the Indo-Pacific region. The shrimp industry is now threatened by diseases and depletion of the wild broodstock. While past research efforts have been on shrimp pathogens, the information about the host P. monodon remains scanty. Basic knowledge of shrimp biology, particularly with regard to the control of growth, reproduction and the immune system, is limited and hampered by the lack of genome information. So far, a number of P. monodon EST projects have been undertaken, and only a small number of P. monodon genes derived from these EST data have been cloned and characterized. We therefore constructed a fosmid library with 5X genomic coverage to provide as a useful resource for positional cloning and physical mapping. With this fosmid library, we will focus on identifying genes that play key roles in important biological processes, such as those involved in stress response, immunity, or sex differentiation. The genes that show differential expression patterns after virus infection, various stress treatments (elevated water temperature, low dissolved oxygen or significant reductions in salinity levels), or between different sexes will be our first priorities to screen. The structure and organization of genes will be delineated, including the upstream and downstream regulatory regions. Next, we will take a glimpse of P. monodon genome by a skim sequencing strategy, i.e., obtaining sequence information from a fraction of genome by sequencing a collection of fosmid clones, including those with target genes. Furthermore, we will adopt a population genetics approach to identify the genes or genomic regions subject to natural selection, as they usually are functionally important. We will embark on an initial survey of genetic variation across the genomic regions that have been completely sequenced by extensive sequencing samples from various genetically diverse populations, including Taiwan (TW), the Philippines (PN), Vietnam (VN), Australia (AUS), eastern Thailand (Th-E), western Thailand (Th-W)], and Madagascar (MG) populations. The single nucleotide polymorphism (SNP) maps developed will contribute to identify specific loci with signatures of natural selection, which include a skew in the allele frequency distribution (i.e., an excess of low and/or high frequency derived alleles), reduced or enhanced levels of genetic variation, increased levels of population differentiation, and elevated levels of linkage disequilibrium (LD) relative to neutral expectation. Genes with higher nucleotide diversity (π) may involve in immune response and those with low or even no diversity may be related to essential metabolic mechanisms or developmental processes. And alleles that show long-range LD against a background of short LD might imply the presence of a selective sweep. In summary, understanding P. monodon genome, especially the genetic components of key biological and commercially relevant traits, will help in fostering a genome-era strategy for world shrimp industry to resolve its disease problems and improve the yield and quality of the shrimps.