Bioinformatic approach in the identification of arabidopsis gene homologous in amaranthus

Abstract

Bioinfomatics offers an efficient tool for molecular genetics applications and sequence homology search algorithms became an inevitable part for many different research strategies. Appropriate managing of known data that are stored in public available databases can be used in many ways in the research. Here, we report the identification of RmlC-like cupins superfamily protein DNA sequence than is known in Arabidopsis genome for the Amaranthusplant specie where this sequence was still not sequenced. A BLAST based approach was used to identify the homologous sequences in the nucleotide database and to find suitable parts of the Arabidopsis sequence were primers can be designed. In total, 64 hits were found in nucleotide database for Arabidopsis RmlC-like cupins sequence. A query cover ranged from 10% up to the 100% among RmlC-like cupins nucleotides and its homologues that are actually stored in public nucleotide databases. The most conserved region was identified for matches that posses nucleotides in the range of 1506 up to the 1925 bp of RmlC-like cupins DNA sequence stored in the database. The in silico approach was subsequently used in PCR analysis where the specifity of designed primers was approved. A unique, 250 bp long fragment was obtained for Amaranthus cruentus and a hybride Amaranthus hypochondriacus x hybridus in our analysis. Bioinformatic based analysis of unknown parts of the plant genomes as showed in this study is a very good additional tool in PCR based analysis of plant variability. This approach is suitable in the case for plants, where concrete genomic data are still missing for the appropriate genes, as was demonstrated for Amaranthus.

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

“…A set of ten conserved domains was discovered in identified E2 members. The motif discovery is required to find patterns in nucleotide or protein sequences to understand the structure and function of the molecules in the system 36 . The presence of conserved domains suggests functional identity among tomato E2 candidates and also with human and Arabidopsis.…”

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses inBrassica rapa

“…It is well understood that the diversity among species mainly happens through genes organization in the genome [ 37 ]. The structure and function of molecules in a system can be understand through patterns of motif in the nucleotide or protein sequences [ 39 ]. The patterns for most of the genes were similar in nature and were dominated by 3-4 numbers of intron.…”