Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice

Abstract

We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.

Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data

“…Then, we selected genes showing at least a twofold change in expression in the light or dark and further analyzed the distribution of log 2 fold change for the other oligo(s) for each gene locus, as shown in Table 1. Validation of expression patterns of candidate genes using RT-PCR For the first-strand cDNA synthesis, 100 ng of mRNAs from the same RNA samples used for the microarray experiments was reverse-transcribed in a total volume of 50 μl that contained 10 ng of oligo (dT) [12][13][14][15][16][17][18] primer, 2.5 mM dNTP, and 100 units of SuperScript™ III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) in reaction buffer supplied by the manufacturer. PCR reactions were performed in 50 μl volumes in solutions containing 1 μl aliquots of the respective cDNA reaction mixture, 0.2 μM of gene-specific primers, 10 mM dNTPs, one unit of Taq DNA polymerase (Invitrogen), and 10× Taq buffer supplied by the manufacturer.…”

“…Alternatively, spliced transcripts have been experimentally identified in large numbers through de novo sequencing methods such as conventional expressed sequence tag (EST) sequencing and massively parallel signature sequencing [17,20,21,25]. Oligonucleotide microarray analysis of expression patterns associated with alternatively spliced transcripts has often been used in studies of human disease but has not been widely applied in plants [10,19,31].…”

Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions

“…AP005199.3: gene no. P0627E10.30) and has not been functionally characterized (Kikuchi et al 2003). Based on the sequence information of the Japanese RGP (GenBank accession no.…”

Update and challenges on proteomics in rice

“…Recently, the International Rice Genome Sequencing Project [7] presented a map-based, finished-quality sequence that covers 95% of the 389-Mb genome of rice, including virtually all of the euchromatin and two complete centromeres. The annotation of rice genomes has progressed at a rapid pace during the past few years so that currently a majority of the predicted genes are supported by full-length cDNAs [8]. Once the rice genome is completely sequenced, the challenge ahead for the monocot plant research community will be to identify the function, regulation, and type of PTM of each encoded protein or proteinprotein interaction.…”