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

Abstract

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 (At) and D sub-genome (Dt), 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, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis

“…Only one ortholog pair and one paralog pair have a ω ratio larger than 1 ( Figure 5 b,d), suggesting that novel functions were likely to generate among these genes. This is the same as some other gene families in plants, such as TCS of tomato, GRAS of Medicago truncatula , and NF-YB of Gossypium hirsutum , of which most homolog pairs evolve through purifying selection and few or even no gene experience positive selection [ 55 , 56 , 57 ].…”

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

“…However, most of the duplicated ANN genes were retained after the whole-genome duplication (WGD) event in B. napus. WGD event of gene family appears to be a widespread phenomenon, such as the auxin response factor (ARF) 47 , Auxin/Indoleacetic acid (Aux/IAA) 48 , glutathione transferases (GST) 49 , BRI1-EMS-SUPPRESSOR1 (BES1) 50 , Heat stress transcription factors (Hsfs) 51,52 , GRAS 53 family genes in diploid and allopolyploid Brassicaceae and Calcium-dependent protein kinases (CPK) 54 , Jasmonate ZIM-domain (JAZ) 55 and Nuclear factor YB (NF-YB) 56 in diploid and allopolyploid Gossypium species (G. raimondii: DD genome; G. arboretum: AA genome; G. hirsutum: AADD genome). Among the 51 Brassica ANN genes, 35 were the typical ANN, which encoded proteins ranging from 315-325 amino acids (AA) and contained four annexin repeats.…”

Identification, Structural Characterization and Gene Expression Analysis of Members of the Nuclear Factor-Y Family in Chickpea (Cicer arietinum L.) under Dehydration and Abscisic Acid Treatments

“…The Nuclear Factor-Y (NF-Y) TFs, which compose of NF-YA, NF-YB and NF-YC subclass TFs, have been shown to be involved in regulation of many developmental processes and responses to various environmental stimuli [ 11 , 12 , 13 , 14 ]. With the great advances in the ‘omics’ era, members of the NF-Y TF family have been identified and characterized in several plant species, including monocotic species, such as common wheat ( Triticum aestivum ) [ 15 ], rice ( Oryza sativa ) [ 16 , 17 ], Brachypodium distachyon [ 18 ], barley ( Hordeum vulgare ) [ 19 ], foxtail millet ( Setaria italica ) [ 20 ], maize ( Zea mays ) [ 21 , 22 ] and sorghum ( Sorghum bicolor ) [ 23 ], as well as dicotic species, such as Arabidopsis thaliana [ 24 , 25 ], common bean ( Phaseolus vulgaris ) [ 26 ], canola ( Brassica napus ) [ 27 , 28 ], soybean ( Glycine max ) [ 29 ], grape ( Vitis vinifera ) [ 30 ], tomato ( Solanum lycopersicum ) [ 31 ], upland cotton ( Gossypium hirsutum ) [ 32 ], sweet orange ( Citrus sinensis ) [ 33 ], and castor bean ( Ricinus communis ) [ 34 ]. However, the NF-Y TFs have not been systematically identified and characterized yet at a genome-wide level in the economically important chickpea, even though its genome sequence has been publically available to the research community for several years [ 35 , 36 ].…”