Project description:Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.
Project description:The chloroplast (cp) genome sequence of Rhizophora apiculata was characterized. The cp genome length was 164,343 bp in length, containing a typical structure of a large single copy (LSC) of 93,155 bp, a small single copy (SSC) of 19,376 bp, and two inverted repeats (IRs) of 25,906 bp, with a GC content of 34.9%. There were 131 genes were annotated in the cp genome, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis using cp genomes of mangroves and ecologically associated species resolved R. apiculata in Rhizophora with R. stylosa and R. x lamarckii. This complete chloroplast sequence offers a promising tool for further species identification and evolutionary studies of Rhizophora, as well as for mangroves.
