[Show abstract][Hide abstract] ABSTRACT: 1 R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.
Full-text · Article · Jun 2015 · Scientific Reports
[Show abstract][Hide abstract] ABSTRACT: MYB proteins constitute one of the largest of transcription factor families in plants. Recently, evidence is accumulation to prove the MYB-related genes play crucial roles in plants. However, little is known about the complex evolutionary history of MYB-related proteins in plants, compared to R2R3-MYB type. Here, we present a genome-wide analysis of MYB-related proteins from 16 species of ﬂowering plants, moss, Selaginella, and algaes. We identified many MYB-related proteins in angiosperms, but few in algaes. Phylogenetic analysis revealed that MYB-related proteins can be classified into 5 distinct subgroups, supported by highly conserved intron patterns, consensus motifs, and architectures of protein domains. Among which, CCA1-like/R-R and TBP-like subgroups were more than 1 billion years old, while I-box-like and CPC-like subgroups were newly derived in angiosperms. We revealed that the MYB-like domain has evolved under strong purifying selection, indicating the conservation of MYB-related proteins. We hypothesize the diversity of MYB-related proteins through three major expansions and domain shuffling, but subsequently retained relatively conserved throughout plant evolution. Expression analysis revealed that the MYB-related gene family has a wide expression profile in maize and soybean development, and has important roles in both development and stress response.
[Show abstract][Hide abstract] ABSTRACT: MYB proteins constitute one of the largest transcription factor families in plants. Recent evidence revealed that MYB-related genes play crucial roles in plants. However, compared with the R2R3-MYB type, little is known about the complex evolutionary history of MYB-related proteins in plants. Here, we present a genome-wide analysis of MYB-related proteins from 16 species of ﬂowering plants, moss, Selaginella, and algae. We identified many MYB-related proteins in angiosperms, but few in algae. Phylogenetic analysis classified MYB-related proteins into five distinct subgroups, a result supported by highly conserved intron patterns, consensus motifs, and protein domain architecture. Phylogenetic and functional analyses revealed that the Circadian Clock Associated 1-like/R-R and Telomeric DNA-binding protein-like subgroups are >1 billion yrs old, whereas the I-box-binding factor-like and CAPRICE-like subgroups appear to be newly derived in angiosperms. We further demonstrated that the MYB-like domain has evolved under strong purifying selection, indicating the conservation of MYB-related proteins. Expression analysis revealed that the MYB-related gene family has a wide expression profile in maize and soybean development and plays important roles in development and stress responses. We hypothesize that MYB-related proteins initially diversified through three major expansions and domain shuffling, but remained relatively conserved throughout the subsequent plant evolution.
[Show abstract][Hide abstract] ABSTRACT: The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no genome-wide characterization of this gene family has been conducted in a legume species. Here we report the first genome-wide analysis of the whole MYB superfamily in a legume species, soybean (Glycine max), including the gene structures, phylogeny, chromosome locations, conserved motifs, and expression patterns, as well as a comparative genomic analysis with Arabidopsis.
A total of 244 R2R3-MYB genes were identified and further classified into 48 subfamilies based on a phylogenetic comparative analysis with their putative orthologs, showed both gene loss and duplication events. The phylogenetic analysis showed that most characterized MYB genes with similar functions are clustered in the same subfamily, together with the identification of orthologs by synteny analysis, functional conservation among subgroups of MYB genes was strongly indicated. The phylogenetic relationships of each subgroup of MYB genes were well supported by the highly conserved intron/exon structures and motifs outside the MYB domain. Synonymous nucleotide substitution (dN/dS) analysis showed that the soybean MYB DNA-binding domain is under strong negative selection. The chromosome distribution pattern strongly indicated that genome-wide segmental and tandem duplication contribute to the expansion of soybean MYB genes. In addition, we found that ~ 4% of soybean R2R3-MYB genes had undergone alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Comparative expression profile analysis of R2R3-MYB genes in soybean and Arabidopsis revealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function.
In this study we identified the largest MYB gene family in plants known to date. Our findings indicate that members of this large gene family may be involved in different plant biological processes, some of which may be potentially involved in legume-specific nodulation. Our comparative genomics analysis provides a solid foundation for future functional dissection of this family gene.
[Show abstract][Hide abstract] ABSTRACT: MYB proteins comprise a large family of plant transcription factors, members of which perform a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). In the present study, we performed a comprehensive computational analysis, to yield a complete overview of the R2R3-MYB gene family in maize, including the phylogeny, expression patterns, and also its structural and functional characteristics. The MYB gene structure in maize and Arabidopsis were highly conserved, indicating that they were originally compact in size. Subgroup-specific conserved motifs outside the MYB domain may reflect functional conservation. The genome distribution strongly supports the hypothesis that segmental and tandem duplication contribute to the expansion of maize MYB genes. We also performed an updated and comprehensive classification of the R2R3-MYB gene families in maize and other plant species. The result revealed that the functions were conserved between maize MYB genes and their putative orthologs, demonstrating the origin and evolutionary diversification of plant MYB genes. Species-specific groups/subgroups may evolve or be lost during evolution, resulting in functional divergence. Expression profile study indicated that maize R2R3-MYB genes exhibit a variety of expression patterns, suggesting diverse functions. Furthermore, computational prediction potential targets of maize microRNAs (miRNAs) revealed that miR159, miR319, and miR160 may be implicated in regulating maize R2R3-MYB genes, suggesting roles of these miRNAs in post-transcriptional regulation and transcription networks. Our comparative analysis of R2R3-MYB genes in maize confirm and extend the sequence and functional characteristics of this gene family, and will facilitate future functional analysis of the MYB gene family in maize.
[Show abstract][Hide abstract] ABSTRACT: Assessment of yield stability is an important issue for maize (Zea mays L.) cultivar evaluation and recommendation. Many parametric procedures are available for stability analysis, each of them allowing for different interpretations. The objective of the present study was to assess yield stability of maize hybrids evaluated in the National Maize Cultivar Regional Trials in southwestern China using 20 parametric stability statistics proposed by various authors at different times, and to investigate their interrelationships. Two yield datasets were obtained from the 2003 and 2004 national maize cultivar regional trials in southwestern China. A combined analysis of variance, stability statistics, and rank correlations among these stability statistics were determined. Effects of location, cultivar, and cultivar by location interaction were highly significant (P
No preview · Article · Sep 2011 · Agricultural Sciences in China
[Show abstract][Hide abstract] ABSTRACT: Analysis of multi-environment trials (METs) of crops for the evaluation and recommendation of varieties is an important issue in plant breeding research. Evaluating on the both stability of performance and high yield is essential in MET analyses. The objective of the present investigation was to compare 11 nonparametric stability statistics and apply nonparametric tests for genotype-by-environment interaction (GEI) to 14 maize (Zea mays L.) genotypes grown at 25 locations in southwestern China during 2005. Results of nonparametric tests of GEI and a combined ANOVA across locations showed that both crossover and noncrossover GEI, and genotypes varied highly significantly for yield. The results of principal component analysis, correlation analysis of nonparametric statistics, and yield indicated the nonparametric statistics grouped as four distinct classes that corresponded to different agronomic and biological concepts of stability. Furthermore, high values of TOP and low values of rank-sum were associated with high mean yield, but the other nonparametric statistics were not positively correlated with mean yield. Therefore, only rank-sum and TOP methods would be useful for simultaneously selection for high yield and stability. These two statistics recommended JY686 and HX168 as desirable and ND108, CM12, CN36, and NK6661 as undesirable genotypes.
No preview · Article · Oct 2010 · Agricultural Sciences in China
[Show abstract][Hide abstract] ABSTRACT: The waxy (wx) locus of Zea mays L. encodes a granule-bound starch synthase (GBSS I = waxy protein) required for the synthesis of amylose in endosperm and pollen grain. This review covers recent advances in understanding the waxy locus in maize, focusing particularly on the new information on mutant type and mutation mechanisms. The results showed that the insertion and deletion played an important role in the generation of spontaneous wx-mutations. The current status of utilizing waxy locus has been summarized and the perspectives of the further studies on this locus have also been proposed.
No preview · Article · Jan 2010 · Agricultural Sciences in China
[Show abstract][Hide abstract] ABSTRACT: MYB genes are widely distributed in higher plants and comprise one of the largest transcription factors, which are characterized by the presence of a highly conserved MYB domain at their N-termini. Over recent decades, biochemical and molecular characterizations of MYB have been extensively studied and reported to be involved in many physiological and biochemical processes. This review describes current knowledge of their structure characteristic, classification, multi-functionality, mechanism of combinational control, evolution, and function redundancy. It shows that the MYB transcription factors play a key role in plant development, such as secondary metabolism, hormone signal transduction, disease resistance, cell shape, organ development, etc. Furthermore, the expression of some members of the MYB family shows tissue-specificity.
Full-text · Article · Feb 2009 · Biochemistry (Moscow)
[Show abstract][Hide abstract] ABSTRACT: Transcriptional regulation of defense gene expression is a crucial part of plant defense responses in plant defense environment stresses. As one of the largest plant transcription factor families, MYB (v-myb avian myeloblastosis viral on-cogene homolog) transcription factors play an important role in plant stress tolerance. In this paper, we review the structural features, functional characterization and molecular mechanism of MYB transcription factor family, and discuss the regula-tory roles of transcription factors in plant defense responses.
No preview · Article · Nov 2008 · Hereditas (Beijing)
[Show abstract][Hide abstract] ABSTRACT: Plant R2R3-myb genes are widely distributed in higher plants and comprise one of the largest known families of regulatory proteins. On the basis of their conserved DNA-binding domain, 2 MYB-like genes, designated GmMYBJ6 and GmMYBJ7 (GenBank accession No. DQ902863 and DQ902864), were cloned from soybean (Glycine max L.) cultivar Jilin 3 using reverse transcription PCR (RT-PCR) and rapid application of cDNA ends (RACE) methods. These genes contained an open reading frame (ORF) of 786 and 969 bp in length encoding 261 and 322 amino acids, respectively. Genomic DNA sequence analysis showed that both genes contained 2 introns. The 2 genes expressed in roots, stems, leaves, flowers, and immature seeds of soybean through semiquantitative RT-PCR analysis, and 2 MYB proteins had transcriptional activation functions detected by yeast one-hybrid assay. However, the activities of transcription were lower when the introns existed. Fluorescence real-time quantification PCR analysis indicated that the expression of GmMYBJ6 and GmMYBJ7 genes were induced by abscisic acid (ABA) and naphthalene acetic acid (NAA), and their expressions were changed with the inducible time. It is concluded that GmMYBJ6 and GmMYBJ7 genes isolated from soybean are new members of MYB transcription factor family, which may play key roles in the signal transduction pathways related to ABA and NAA in soybean.
[Show abstract][Hide abstract] ABSTRACT: Amylose, amylopectin and starch dynamic accumulation and key enzymes activities in the grains of 4 maize inbred lines (two high-starch ones and two low-starch ones) were studied. The amounts of amylose, amylopectin and starch in the grains of 4 maize inbred lines increased as sigmoid curves during grain filling period. The changes in amylose, amylopectin and starch accumulation rates followed single-peaked curves, and reached their peaks in the 25-30 days after pollination (DAP). Changes in activities of adenosine diphosphoglucose pyrophosphorylase (ADPG-PPase, EC 126.96.36.199), soluble starch synthase (SSS, EC 188.8.131.52) and starch granule-bound synthase (GBSS, EC 184.108.40.206) in the grains of 4 inbred lines appeared single-peaked curves with the peaks appearing 20-30 DAP. Changes in activities of starch-branching enzyme (Q-enzyme, EC 220.127.116.11) in the grains of high-starch inbred lines appeared single-peaked curves with the peak values at 20 DAP, while the two low-starch inbred lines showed double-peaked curves with the peak values in the 15-20 DAP and 30-35 DAP. There was significant correlation between ADPG-PPase, SSS and GBSS activities. The results indicated that the Q-enzyme had different expression in high- and low-starch maize inbred lines, and verified that ADPG-PPase, SSS and GBSS activities were significantly and positively correlated with amylose, amylopectin and starch accumulation rates.
No preview · Article · May 2007 · Zhi wu sheng li yu fen zi sheng wu xue xue bao = Journal of plant physiology and molecular biology