Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa

Abstract

Trihelix genes play important roles in plant growth and development and responses to biotic and abiotic stresses. Here, we identified 56 full-length trihelix genes in Populus trichocarpa and classified them into five groups. Most genes within a given group had similar gene structures and conserved motifs. The trihelix genes were unequally distributed across 19 different linkage groups. Fifteen paralogous pairs were identified, 14 of which have undergone segmental duplication events. Promoter cis-element analysis indicated that most trihelix genes contain stress- or phytohormone-related cis-elements. The expression profiles of the trihelix genes suggest that they are primarily expressed in leaves and roots. Quantitative real-time reverse transcription polymerase chain reaction analysis indicated that members of the trihelix gene family are significantly induced in response to osmotic, abscisic acid, salicylic acid, methyl jasmonate and pathogen infection. PtrGT10 was identified as a target gene of miR172d, which is involved in the osmotic response. Repression of PtrGT10 could increase reactive oxygen species scavenging ability and decrease cell death. This study provides novel insights into the phylogenetic relationships and functions of the P. trichocarpa trihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

Peer Review #2 of "Characterization of the basic helix–loop–helix gene family and its tissue-differential expression in response to salt stress in poplar (v0.1)"

“…In addition, each group shares similar intron and exon structures. These results of motif and gene structure analysis are similar to the study of the poplar trihelix family (Wang et al 2016). The previous study found that the domains outside the bHLH domain may have diverse molecular functions in Arabidopsis (Toledo-Ortiz et al 2003).…”

Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

“…Interestingly, OsTIFY1a, -1b, -2a, -2b, AtTIFY1, -2a, -2b not only have a TIFY domain but also a GATA zinc-finger and a CCT motif; the remaining members in Rice and Arabidopsis do not have the CCT motif. However, almost all the PtrZML proteins contain the CCT motif, suggesting that woody plants might have undergone many different changes during the evolutionary process [37].…”

Genome wide identification of the trihelix transcription factors and overexpression of Gh_A05G2067 (GT‐2), a novel gene contributing to increased drought and salt stresses tolerance in cotton

“…The number of trihelix found in the various cotton species is in agreement with previous findings, in which the members of the trihelix family have been found to be relatively low compared to other plant TFs family, such as MYBs, despite that trihelix genes are believed to have evolved from the MYBs (Nagano ). To date, 30, 31, 52 and 80 trihelix gene members have been identified in Arabidopsis (Kaplan‐Levy et al ), Oryza sativa (Qin et al ), Brassica rapa (Wang et al ) and Populus trichocarpa (Wang et al ), respectively. The low numbers of the trihelix genes in plants show that they are the most recent genes to evolve, and this could be linked to the environmental changes the plants are currently being exposed to.…”