Transcriptomic Study On Date Palm Fruiting&Two Kinds Of Aquatic Creatures

Abstract:The transcriptome is the set of all RNA molecules produced in one or a population of cells. And the term can be applied to the total set of transcripts including mRNA transcript expression analysis-full-length mRNA and expressed sequence tags (ESTs), novel gene discovery, gene space identification in novel genomes, singlenucleotide polymorphism (SNP), insertion-deletion and splice-variant discovery, as well as analyses of allele-specific expression and chromosomal rearrangement. Now, the trancsriptome approach has formed four major categories; with the declining costs as well as the updating technology, transcroptome has been widely applied to various genomics research, and it has greatly promoted the development of molecular biology. And this thesis is mainly about bioinformatics analysis based on transcriptome sequencing.1. A transcriptome study of fruiting from Date palmDate, with very high sugar content, is the staple food of the Middle East for thousands of years. In order to explore the important maturation mechanism, we constructed7rapid cDNA libraries, and sequenced by using Roche GS FLX. Finally, we got more than1million reads per tissue and a total number of more than7.6million reads with an average length of361bp. In this study, we assemble the data by using Newbler2.5, and annotated the isotigs we got. Based on sequence similarities,10core cell cycle genes,18genes associated with fruit ripening, and7genes related to starch metabolism were identified. From cluster analysis of metabolic pathways, each pathway in the fruit development has a significant change. Especially the carbohydrate metabolism is particularly prominent during fruit ripening. Of particular note is that sugar synthesis pathways are very active in the critical period of fruit ripening. Additionally, the expression level of Fructose-bisphosphate aldolase increase sharply during fruit ripening, and the gene may play a very important role in the sugar synthesis in dates.2. cDNA library construction and bioinformatics analysis from hemocytes of Triangle sail musselTriangle sail mussel (Hyriopsis cumingii) is the most important mussel species commercially exploited for freshwater pearl production in China. The objectives of this study were to identify genes involved in defense mechanisms, and to identify polymorphic markers from the expressed sequence tag (EST) resources for genetic analysis. A total of5,290ESTs were sequenced, obtaining481contigs and1,165singletons. Based on sequence similarities,50genes were identified as putative genes involved in immune and defense functions. A total of201microsatellites were identified from these ESTs, with31having sufficient flanking sequences for primer design, and14of them were polymorphic.987putative single nucleotide polymorphisms were identified including204transitions,611transversions, and172indels;12of them were involved in nine genes of defense mechanisms. These resources provide the material basis for future marker validation and genetic linkage and quantitative trait loci analysis in the freshwater pearl mussel.3. A transcriptome comparative analysis between nutrition and reproduction from Mitten crabThe mitten crab (Eriocheir sinensis) is one of the most important aquaculture species in China. And this study aims to chase the delicate relationship between nutrition and reproduction. We acquired6287high quality expressed sequence tags (3297from hepatopancreas and2290form testis), representing3829unigenes totally. Genes most likely expressed more frequently and localized in hepatopancreas, and abundant genes from testis for multiple functions. Among these genes, alignment of leptin receptor-like protein and vasa-like protein from mitten crab and other species showed even more genomic information on mitten crab. We identified seventeen genes relevant to control of nutrition mechanisms and eleven genes involved in regulation of reproduction. And this study provides insights into the genetic and molecular mechanisms of nutrition and reproduction in the crab. Such information would facilitate the optimization of breeding in the aquaculture of mitten crabs.