Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz)

Abstract

Plant-specific TIFY [TIF(F/Y)XG] proteins serve important roles in the regulation of plant stress responses. This family encodes four subfamilies of proteins, JAZ (JASMONATE ZIM-domain), PPD (PEAPOD), ZML (Zinc-finger Inflorescence-like), and TIFY. In this work, a total of 16 JAZ, 3 PPD, 7 ZML, and 2 TIFY genes were found in cassava (Manihot esculenta Crantz) at the genome-wide level. The phylogenetics, exon-intron structure, motif organization, and conserved domains of these genes were analyzed to characterize the members of the JAZ, PPD, and ZML subfamilies. Chromosome location and synteny analyses revealed that 26 JAZ, PPD, and ZML genes were irregularly distributed across 14 of the 18 chromosomes, and 18 gene pairs were implicated in large-scale interchromosomal segmental duplication events. In addition, JAZ, PPD, and ZML gene synteny comparisons between cassava and three other plant species (Arabidopsis, Populus trichocarpa, and rice) uncovered vital information about their likely evolution. The prediction of protein interaction network and cis-acting elements reveal the function of JAZ, PPD, and ZML genes. Subsequently, expression patterns of JAZ, PPD, and ZML genes were validated by qRT-PCR as being expressed in response to osmotic, salt, and cadmium stress. Moreover, almost all JAZ subfamily genes were responsive to jasmonic acid (JA) treatment. In particular, MeJAZ1, MeJAZ13, and MeJAZ14, were highly up-regulated by three treatments, and these genes may deserve further study. This comprehensive study lays the groundwork for future research into TIFY family genes in cassava and may be valuable for genetic improvement of cassava and other related species.

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

“…Almost all MeSRS genes were upregulated following PEG and NaCl treatments ( Figure 9 ), suggesting that they play a role in the regulation of diverse stress-related responses. Interestingly, the changes in gene expression and time across various treatments are not simple linear connections, indicating that the regulation of distinct MeSRS family members is a complex process, as corroborated by other studies [ 28 , 47 ]. Although our findings suggest that the MeSRS genes respond to phytohormone stimulation and abiotic stress, much more research is required to fully understand this response mechanism.…”

“…Fragments per kilobase of transcript per million reads mapped (FPKM) values were calculated to evaluate the gene expression. Log 2 -transformed heatmaps of all MeSRS genes were produced using TBtools software [ 47 ].…”

Genome-wide identification of thaumatin-like protein family genes in Panax notoginseng and analysis of their responses to Fusarium solani infection

“…Among the hormone response elements, MeJA and ABA response elements are numerously, and a few other hormone response components. A number of plant hormones, including ABA, SA, and JA, have a role in stress reactions by triggering the transcription of genes involved in defense(Zheng, Wan, et al, 2022). Which shown that PnTLPs may be susceptible to MeJA and ABA regulation and thus play a role in plant growth and development as well as in adversity stress, which is generally consistent with the studies in watermelon(Ram, Danish, et al, 2022), woodland strawberry, and Hickory(Li, Xu, et al,…”

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

“…In this study, the number of proteins identified from the E. japonica genome, 26, was greater than the TIFY proteins in P. persica [ 2 ], A. thaliana [ 4 ], P. trichocarpa [ 12 ], O. sativa [ 10 ], and V. viniferas [ 7 ]; however, it was less than that in M. domestica [ 11 ], G. max [ 26 ], Manihot esculenta Crantz [ 43 ], and Brassica napus [ 45 ]. Gene duplication events are the main drivers of rapid gene family expansion and evolution.…”