Evolution and co-evolution: insights into the divergence of plant heat shock factor genes

Parakkunnel, Ramya; Naik, K. Bhojaraja; Susmita, C.; Girimalla, Vanishree; Bhaskar, K. Udaya; Sripathy, K. V.; Shantharaja, CS; Aravindan, S; Kumar, Satyendra; Bhat, K. V.

doi:10.1007/s12298-022-01183-7

Cited by 4 publications

(3 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One 11 intron T2C sub-family gene was found to be conserved in the genome without any change in exonic sequences although size variation was noticed for the 2 nd intron. Enhanced gene copy number, as well as the predominance of large genes with multiple exons in the genome of Swetha, was reported earlier for TCP (Parakkunnel et al, 2020) and HSF (Parakkunnel et al, 2022) gene families in sesame.…”

Section: Discussionsupporting

confidence: 66%

“…The duplication of parental genes prior to fusion was evident also in the sesame genome (Zhou et al, 2022b) while most of the added domains were products of horizontal transfer. In sesame, gene fusion and creation of novel multi-domain genes were reported in HSF genes (Parakkunnel et al, 2022) while the fusion with retrotransposons were reported for TCP genes (Parakkunnel et al, 2020). Selection effects were significant for 21 fusion genes in sesame wherein positive selection was noticed in >71% of genes in contrast to the rice genome (Zhou et al, 2022b).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Parakkunnel¹,

K²,

Girimalla³

et al. 2022

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.

show abstract

Section: Discussionsupporting

confidence: 66%

Section: Discussionmentioning

confidence: 99%

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Parakkunnel¹,

K²,

Girimalla³

et al. 2022

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although Lchi22185 has no conserved domain sequence, it nonetheless can be clustered within the AtAHL evolutionary tree. Genome duplications, non-neutral selection, and co-evolving residues may lead to changes in the conserved domain of proteins [ 37 ]. Thus, we speculate that Lchi22185 may have lost its conserved domain during evolution.…”

Section: Discussionmentioning

confidence: 99%

AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis

Tang

Zheng³

et al. 2023

Plants

View full text Add to dashboard Cite

AT-hook motif nuclear localized (AHL) is a transcription factor that can directly induce plant somatic embryogenesis without adding exogenous hormones. One of its functional domains, the AT-hook motif, has a chromatin-modifying function and participates in various cellular processes, including DNA replication and repair and gene transcription leading to cell growth. Liriodendron chinense (Hemsl.) Sargent is an important ornamental and timber tree in China. However, its low drought-resistant ability further leads to a low natural growth rate of its population. Based on bioinformatics analysis, this study identified a total of 21 LcAHLs in L. chinense. To explore the expression pattern of the AHL gene family under drought and somatic embryogenesis, we performed a systematic analysis including basic characteristics, gene structure, chromosome localization, replication event, cis-acting elements and phylogenetic analyses. According to the phylogenetic tree, the 21 LcAHL genes are divided into three separate clades (Clade I, II, and III). Cis-acting element analysis indicated the involvement of the LcAHL genes in drought, cold, light, and auxin regulation. In the generated drought stress transcriptome, a total of eight LcAHL genes showed increased expression levels, with their expression peaking at 3 h and leveling off after 1 d. Nearly all LcAHL genes were highly expressed in the process of somatic embryogenesis. In this study, we performed a genome-wide analysis of the LcAHL gene family and found that LcAHLs take part in resistance to drought stress and the development of somatic embryos. These findings will provide an important theoretical basis for understanding of the LcAHL gene function.

show abstract

Integrated transcriptomic and proteomic analysis unravels the response mechanisms of Saccharina japonica to heat stress

Lin,

Liu,

Lin

et al. 2025

Aquaculture

View full text Add to dashboard Cite

Evolution and co-evolution: insights into the divergence of plant heat shock factor genes

Cited by 4 publications

References 68 publications

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis

Integrated transcriptomic and proteomic analysis unravels the response mechanisms of Saccharina japonica to heat stress

Contact Info

Product

Resources

About