title: Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum.
abstract: Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
authors.forename: Aleena
authors.initials: A
authors.lastname: Francis
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
authors.forename: Namrata
authors.initials: N
authors.lastname: Dhaka
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
authors.forename: Mohit
authors.initials: M
authors.lastname: Bakshi
authors.affiliation: Graduate School of Biotechnology &Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.affiliation: School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
authors.forename: Manoj K
authors.initials: MK
authors.lastname: Sharma
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India.
authors.forename: Rita
authors.initials: R
authors.lastname: Sharma
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D023281:Genomics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D006109:Poaceae / Q000235:genetics; D017423:Sequence Analysis, RNA; D045868:Sorghum / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics; D013347:Subcellular Fractions / Q000378:metabolism
chemical_list: D010940:Plant Proteins