Identification and characterization of NF-YB family genes in tung tree

Comprehensive Analysis of the NF-YB Gene Family and Expression under Abiotic Stress and Hormone Treatment in Larix kaempferi

NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have not yet been explored in Larix kaempferi, a tree species with high economic and ecological values in northeast China and other regions, limiting the breeding of anti-stress L. kaempferi. In order to explore the roles of NF-YB transcription factors in L. kaempferi, we identified 20 LkNF-YB family genes from L. kaempferi full-length transcriptome data and carried out preliminary characterization of them through series of analyses on their phylogenetic relationships, conserved motif structure, subcellular localization prediction, GO annotation, promoter cis-acting elements as well as expression profiles under treatment of phytohormones (ABA, SA, MeJA) and abiotic stresses (salt and drought). The LkNF-YB genes were classified into three clades through phylogenetic analysis and belong to non-LEC1 type NF-YB transcription factors. They have 10 conserved motifs; all genes contain a common motif, and their promoters have various phytohormones and abiotic stress related cis-acting elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the sensitivity of the LkNF-YB genes to drought and salt stresses was higher in leaves than roots. The sensitivity of LKNF-YB genes to ABA, MeJA, SA stresses was much lower than that to abiotic stress. Among the LkNF-YBs, LkNF-YB3 showed the strongest responses to drought and ABA treatments. Further protein interaction prediction analysis for LkNF-YB3 revealed that LkNF-YB3 interacts with various factors associated with stress responses and epigenetic regulation as well as NF-YA/NF-YC factors. Taken together, these results unveiled novel L. kaempferi NF-YB family genes and their characteristics, providing the basic knowledge for further in-depth studies on their roles in abiotic stress responses of L. kaempferi.

Genome-wide screening and identification of nuclear Factor-Y family genes and exploration their function on regulating abiotic and biotic stress in potato (Solanum tuberosum L.)

The Nuclear Factor-Y (NF-Y) transcription factor (TF), which includes three distinct subunits (NF-YA, NF-YB and NF-YC), is known to manipulate various aspects of plant growth, development, and stress responses. Although the NF-Y gene family was well studied in many species, little is known about their functions in potato. In this study, a total of 37 potato NF-Y genes were identified, including 11 StNF-YAs, 20 StNF-YBs, and 6 StNF-YCs. The genetic features of these StNF-Y genes were investigated by comparing their evolutionary relationship, intron/exon organization and motif distribution pattern. Multiple alignments showed that all StNF-Y proteins possessed clearly conserved core regions that were flanked by non-conserved sequences. Gene duplication analysis indicated that nine StNF-Y genes were subjected to tandem duplication and eight StNF-Ys arose from segmental duplication events. Synteny analysis suggested that most StNF-Y genes (33 of 37) were orthologous to potato's close relative tomato (Solanum lycopersicum L.). Tissue-specific expression of the StNF-Y genes suggested their potential roles in controlling potato growth and development. The role of StNF-Ys in regulating potato responses to abiotic stress (ABA, drought and salinity) was also confirmed: twelve StNF-Y genes were up-regulated and another two were down-regulated under different abiotic treatments. In addition, genes responded differently to pathogen challenges, suggesting that StNF-Y genes may play distinct roles under certain biotic stress. In summary, insights into the evolution of NF-Y family members and their functions in potato development and stress responses are provided.

NF-YB-Mediated Active Responses of Plant Growth under Salt and Temperature Stress in Eucalyptus grandis

The transcription factor NF-YB (nuclear factor-YB) family is a subfamily of the nuclear factor Y (NF-Y), which plays an important role in regulating plant growth, development and participates in various stress responses. Although the NF-Y family has been studied in many species, it is still obscure in Eucalyptus grandis. In this study, 23 EgNF-YB genes in eucalyptus were identified and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed the EgNF-YB genes were divided into two clades, LEC-1 type and non-LEC1 type. The evolution of distinct clades was relatively conservative, the gene structures were analogous, and the differences of genetic structures among clades were small. The expression profiles showed that the distinct EgNF-YB genes were highly expressed in diverse tissues, and EgNF-YB4/6/13/19/23 functioned in response to salinity, heat and cold stresses. Our study characterized the phylogenetic relationship, gene structures and expression patterns of EgNF-YB gene family and investigated their potential roles in abiotic stress responses, which provides solid foundations for further functional analysis of NF-YB genes in eucalyptus.

Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis

Members of the NF-YB transcription factor gene family play important roles in diverse processes related to plant growth and development, such as seed development, drought tolerance, and flowering time. However, the function of NF-YB genes in cotton remains unclear. A total of 23, 24, and 50 NF-YB genes were identified in Gossypium arboreum (G. arboreum), Gossypium raimondii (G. raimondii), and G. hirsutum, respectively. A systematic phylogenetic analysis was carried out in G. arboretum, G. raimondii, G. hirsutum, Arabidopsis thaliana, cacao, rice and, sorghum, where the 150 NF-YB genes were divided into five groups (α–ε). Of these groups, α is the largest clade, and γ contains the LEC1 type NF-YB proteins. Syntenic analyses revealed that paralogues of NF-YB genes in G. hirsutum exhibited good collinearity. Owing to segmental duplication within the A sub-genome (A_t) and D sub-genome (D_t), there was an expanded set of NF-YB genes in G. hirsutum. Furthermore, we investigated the structures of exons, introns, and conserved motifs of NF-YB genes in upland cotton. Most of the NF-YB genes had only one exon, and the genes from the same clade exhibited a similar motif pattern. Expression data show that most NF-YB genes were expressed ubiquitously, and only a few genes were highly expressed in specific tissues, as confirmed by quantitative real-time PCR (qRT-PCR) analysis. The overexpression of GhDNF-YB22 gene, predominantly expressed in embryonic tissues, indicates that GhDNF-YB22 may affect embryogenesis in cotton. This study is the first comprehensive characterization of the GhNF-YB gene family in cotton, and showed that NF-YB genes could be divided into five clades. The duplication events that occurred over the course of evolution were the major impetus for NF-YB gene expansion in upland cotton. Collectively, this work provides insight into the evolution of NF-YB in cotton and further our knowledge of this commercially important species.

Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species

Leucine-rich repeat receptor-like kinases (LRR-RLKs) make up the largest group of RLKs in plants and play important roles in many key biological processes such as pathogen response and signal transduction. To date, most studies on LRR-RLKs have been conducted on model plants. Here, we identified 236 and 230 LRR-RLKs in two industrial oil-producing trees: Vernicia fordii and Vernicia montana, respectively. Sequence alignment analyses showed that the homology of the RLK domain (23.81%) was greater than that of the LRR domain (9.51%) among the Vf/VmLRR-RLKs. The conserved motif of the LRR domain in Vf/VmLRR-RLKs matched well the known plant LRR consensus sequence but differed at the third last amino acid (W or L). Phylogenetic analysis revealed that Vf/VmLRR-RLKs were grouped into 16 subclades. We characterized the expression profiles of Vf/VmLRR-RLKs in various tissue types including root, leaf, petal, and kernel. Further investigation revealed that Vf/VmLRR-RLK orthologous genes mainly showed similar expression patterns in response to tree wilt disease, except 4 pairs of Vf/VmLRR-RLKs that showed opposite expression trends. These results represent an extensive evaluation of LRR-RLKs in two industrial oil trees and will be useful for further functional studies on these proteins.