Pipeline publication

[…] n_7.0/all.dir/), foxtail millet (http://foxtailmillet.genomics.org.cn/page/species/download.jsp), and Brachypodium ( ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/brachypodium_distachyon/pep/) were downloaded. The paralogs and orthologs among finger millet, rice, sorghum, maize, foxtail millet, and Brachypodium were identified using OrthoMCL []. The groups having at least one copy of gene from each genome were considered as core orthologous groups (COGs). Based on orthoMCL clustering, protein sequences of single copy ortholog gene groups from six species were aligned and inferred phylogenetic relationship as described previously []. The consensus phylogenetic tree was drawn using FigTree V1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Scaffolds of finger millet genome was concatenated and syntenic relationship among Poaceae species was inferred by Symap tool []. Protein sequences of plant transcription factors (TFs) were retrieved from plant transcription factor database (http://planttfdb.cbi.pku.edu.cn/index.php) and used as a reference to identify TFs in ML-365 genes by BLASTP (default e-value cutoff = 10−10, minimum identity = 40% and minimum query coverage = 50%) alignments., We retrieved gene sequences from NCBI database involved in calcium transporter process based on functional annotation like Ca(2+)/H(+) antiporter (CAX1), two pore channel (TPC1), CaM-stimulated type IIB Ca(2+) ATPase, Calmodulin dependent protein kinase 1 and 2 (CaMK) based on previous studies [, ]. The predicted Finger millet protein sequences were queried against these protein sequences using BLASTP analysis. Also, the genes containing leucine rich repeats (LRR), coiled-coil (CC), protein kinases (PKs) and NB-ARC domains were identified in finger millet predicted gene set based on protein family (Pfam) annotation using InterProScan5 software []. In order to understand the genes involved in C4 mechanism, previously characterized C4 pathway genes from different cereals were used as a reference [, ] to identify C4 genes in finger millet genome. Homologs with highest identity were selected from finger millet sequenced data for each of the seven C4 pathway genes viz., phosphoenolpyruvate carboxylase (PEPC), PEPC kinase (PPCK), NADP-malate dehydrogenase (NADP-MDH), NADP-malic enzyme (NADP-ME), pyruvate orthophosphate dikinase (PPDK), PPDK-regulatory protein (PPDK-RP), and carbonic anhydrase (CA). Ortholog genes from finger millet genome were used for multiple sequence alignment (MSA) and phylogenetic analyses wi […]

Pipeline specifications

Software tools FigTree, SyMAP, BLASTP, InterProScan
Organisms Setaria italica, Oryza sativa
Chemicals Amino Acids, Calcium, Metals, Alkaline Earth, Carbon, Amino Acids, Essential, Amino Acids, Sulfur, Amino Acids, Neutral, Nitrogen, Amino Acids, Essential, Amino Acids, Cyclic