Construction and profiling of a cDNA library from young fruit of satsuma mandarin

To profile gene expression in the early stage of fruit development from ‘Nichinan No. 1’ satsuma mandarin (Citrus unshiu Marc.), we isolated total mRNA at 30 d after flowering. A cDNA library was prepared from mature mRNAs and a total of 2350 cDNA clones were partially sequenced. In all, 1914 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length of 150 nucleotides. A total of 763 unigenes, consisting of 138 contigs and 625 singletons, was identified after assembly of those ESTs. According to our homology search with BLASTX against the NCBI database, the deduced amino acid sequences of 253 unigenes were homologous to proteins with known function and 242 unigenes were significantly matched to proteins with putative or unknown functions. The remaining 268 showed no significant similarity to any protein sequences found in the public database with matches higher than an E value of 10^-5. The 253 unigenes matched to proteins with known function were then manually assigned to 10 cellular functional categories using a modified MIPS MATDB classification. The expression level of each gene was analyzed based on the redundancy of cDNA clones in each contig that comprised more than 10 ESTs. Here, the most abundant gene expressed in young fruits was for a chitinase precursor. A miraculin-like protein and a lectin-related protein precursor were also abundant.     

Generation and analysis of expressed sequence tags from adductor muscle of Japanese scallop Mizuhopecten yessoensis

A normalized cDNA library was constructed from the adductor muscle of M. yessoensis and acquired 4595 high quality expressed sequence tags (ESTs). After clustering and assembly of the ESTs, 3061 unigenes containing 654 contigs and 2407 singletons were identified. The contig length ranged from 266 bp to 2364 bp and the average length of these contigs was 544 bp. Blastx nonredundant protein database analysis showed that 1522 unigenes had significant homology to known genes (E value ≤ 10^? 5). By comparing to Clusters of Orthologous Groups (COG) categories, 460 unigenes were annotated (E value ≤ 10^? 10). Using Kyoto Encyclopedia of Genes and Genomes (KEGG), 345 of 3061 unigenes were assigned into 103 pathways (E value ≤ 10^? 5). For InterProScan searches, 1237 unigenes were annotated containing 727 different types of protein domains. 941 of the 1237 unigenes were annotated for Gene Ontology (GO) classification using Uniprot2GO associations in any category (biological, cellular, and molecular). By sequences comparability and analysis of Blastx NCBI nonredundant protein database and KEGG, 66 unigenes were identified that may be involved in genetic information processing based on the known knowledge. The study provides a material basis as useful information for the genomic analysis of shellfish.