WRKY Genome Analysis in B. juncea

@Kashifniaxi804

Are you expecting WRKY identification strictly from domain-based validation (HMM/Pfam) or should annotated gene models also be included and re-validated? I can deliver a complete, publication-grade in-silico analysis of the WRKY gene family in Brassica juncea, covering accurate gene identification, comparative genomics, and a robust phylogenetic framework. I’ll use a reproducible pipeline combining HMMER + Pfam for domain-confirmed identification, OrthoFinder for orthology/paralogy analysis, and MAFFT with IQ-TREE (1000 bootstraps) for high-confidence phylogeny. Domain, motif (MEME), chromosomal localization, and synteny analyses will also be included. You will receive: • Clean WRKY gene set (FASTA + GFF) • Comparative genomics tables + synteny plots • Publication-ready phylogenetic tree (Newick + annotated figure) • Domain & motif analysis outputs • Chromosomal mapping • Fully documented methods (commands, versions, parameters) • Concise biological interpretation I’ve handled similar genome-scale analyses and ensure results are defensible for publication. Share your genome assembly, annotation, and protein sequences, and I can get started immediately.

@Oluwaferanmio8

You don’t just need a gene list — you need a clean, reproducible pipeline that correctly identifies WRKY members, validates them, and produces publication-ready comparative and phylogenetic outputs. The biggest risk here is inconsistent domain filtering or weak tree construction, which can misclassify genes and weaken your results. I can run a structured in-silico workflow starting with HMMER (Pfam WRKY domain) + BLASTp validation to accurately identify all WRKY genes and extract CDS, protein sequences, and loci. I’ll then use OrthoFinder for orthology/paralogy analysis across Brassica relatives and Arabidopsis, followed by IQ-TREE for robust phylogenetic reconstruction with strong bootstrap support. I’ll also include chromosomal mapping, motif (MEME), and domain analysis for full characterization. You’ll receive: • Reproducible methods report (tools, commands, parameters) • Clean FASTA + GFF files • Comparative genomics tables + synteny plots • Publication-ready phylogenetic tree (Newick + annotated visuals) • Chromosomal location, domain & motif analysis • Clear interpretation summary Timeline: ~7–10 days depending on dataset size. If you want a defendable, publication-ready analysis, message me now and let’s get started.

@Ram0619

Greetings, This is Dr. M. K. Ramkumar. I'm a PhD in Biotechnology with specialization in plant genomics and genetics. I have more 10 years of research experience in the genomics field. I'm enlisting my research publications that align with the expertise you require for the task. 1. Rathinam, M., Ramkumar, M. K., Dokka, N., Senthil, K., Anandkumar, L. H. D., Mathur, V., Tyagi, S., Sitrarasu, S., Parashar, M. and Oraon, P. K. (2025) ‘A chromosome-scale reference genome assembly of pigeonpea wild relative Cajanus platycarpus highlights the evolutionary decline of defence genes in Cajanus cajan’ , Journal of Experimental Botany, 76(20), pp. 6166–6184. 2. Dokka, N., Tyagi, S., Ramkumar, M. K., Rathinam, M., Senthil, K. and Sreevathsa, R. (2024) ‘Genome-wide identification and characterization of DIRIGENT gene family (CcDIR) in pigeonpea (Cajanus cajan L.) provide insights on their spatial expression pattern and relevance to stress response’ , Gene, 914, p. 148417. 3. Kumar, D., Ramkumar, M. K., Dutta, B., Kumar, A., Pandey, R., Jain, P. K., Gaikwad, K., Mishra, D. C., Chaturvedi, K. K. and Rai, A. (2023) ‘Integration of miRNA dynamics and drougacclimation in rice’ , Plants, 12(8), p. 1697. I have my own startup company registered as Gene Counts Laboratory and I have performed multiple genome and transcriptome data analyses in different crops, one of them being Brassica juncea. If my experience is what you require, feel free to contact me.