Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress

• Published in: Scientific reports Vol. 11; no. 1; p. 9177
• Main Authors: Raghavendra, K. P., Das, J., Kumar, R., Gawande, S. P., Santosh, H. B., Sheeba, J. A., Kranthi, S., Kranthi, K. R., Waghmare, V. N.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 28-04-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/449; 631/61; Abiotic stress; Abscisic acid; Climate adaptation; Cotton; Genes; Genomes; Gossypium arboreum; Humanities and Social Sciences; Jasmonic acid; LIM domain proteins; multidisciplinary; Pathogens; Phylogeny; Phytohormones; Plant species; Science; Science (multidisciplinary); Sodium chloride; Ubiquitin; Wilt; Zinc finger proteins
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-87934-0

Asiatic cotton (
Gossypium arboreum
) cultivated as ‘
desi
cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of
G. arboreum
is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of
LIM
gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in
LIM
gene family of the plant species studied, except in
Brassica rapa.
Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X
2
-C-X
17
-H-X
2
-C)-X
2
-(C-X
2
-C-X
17
-C-X
2
-H)] and [(C-X
2
-C-X
17
-H-X
2
-C)-X
2
-(C-X
4
-C-X
15
-C-X
2
-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty
GaLIMs
showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of
GaDA1/DAR
under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (
Fusarium oxysporum
). Expressions patterns of
GaDA1/DAR
showed variable response and identified
GaDA2
as a probable candidate gene for stress tolerance in
G. arboreum.