ABSTRACT: The cell cycle is controlled by the interplay of many different molecules. Foremost in this process are the cyclin family
of proteins that serve to regulate the cell cycle by interacting with cyclin-dependent kinases (CDKs). To date, the cell cycle
and functions of the cyclin gene family have been extensively analyzed in Arabidopsis, rice, and humans. However, the cyclin gene family in poplar has rarely been researched. In the present study, cyclin genes
were predicted in the poplar draft genome sequence by comparison with Arabidopsis cyclin genes, and analyzed by phylogenetic relationships, chromosomal distributions, protein motifs, and expression patterns.
A conserved cyclin_N domain distinguished poplar, and 45 predicted cyclin genes were classified into seven types, including
A-, B-, C-, D-, Q-, T-, and Z-types. Phylogenetic analyses indicated that five of the seven cyclin types were consistent with
Arabidopsis types, the poplar cyclinD gene subfamily exhibited more classes than observed in Arabidopsis and rice, and Q- and Z-types each possessed only one cyclin gene, which we defined as new putative types of poplar cyclin
genes. We selected the special cyclin genes (Q- and Z-types and D3 subgroups) to study the expression patterns in different
tissues by semiquantitative reverse-transcription polymerase chain reaction (RT-PCR). The outcomes indicated that almost all
of the D3 subgroup genes were expressed in various tissues, the Q cyclin gene was detected in roots and stems, and the Z cyclin
gene was only identified in roots. Analysis of the poplar cyclin gene family provides insights into cell cycle mechanisms
and cyclin gene functions.
KeywordsCyclins–Poplar–Phylogenetic analysis–Expression pattern
Plant Cell Tissue and Organ Culture 05/2012; 107(1):55-67. · 3.09 Impact Factor
ABSTRACT: MADS-box genes comprise a large gene family, which codes for transcription factors, and play important functions in various
aspects of flowering plant growth and development. However, little is known about the MADS-box genes in maize (Zea mays) and sorghum (Sorghum bicolor). Here, we performed a comprehensive bioinformatics analysis of the MADS-box gene family in the maize and sorghum genomes
and identified 75 maize and 65 sorghum MADS-box genes. We subsequently carried out a comparative analysis of these genes,
including the gene structure, phylogenetic relationship, conserved protein motifs, gene duplications, chromosomal locations
and expression pattern between the two plants. According to these analyses, the MADS-box genes in both maize and sorghum were
categorized into five (MIKCC, MIKC*, Mα, Mβ and Mγ) groups, and the MIKCC groups were further divided into 11 subfamilies. In addition, gene duplications of MADS-box genes were also investigated
in the maize, sorghum, rice and Arabidopsis genomes. We found a higher percentage of MADS-box gene duplications in the maize and sorghum genomes, which contributed to
the expansion of the MADS-box gene family. Furthermore, both tandem and segmental duplications played a major role in the
MADS-box gene expansion in maize and sorghum. A survey of maize and sorghum EST sequences indicated that MADS-box genes exhibit
a various expression pattern, suggesting diverse and novel functions of MADS-box gene families in the two plants. These results
provided a useful reference for selection of candidate MADS-box genes for cloning and further functional analysis in both
maize and sorghum.
KeywordsMADS-box–Maize–Sorghum–Phylogenetic analysis–Duplication–Expression patterns
Plant Cell Tissue and Organ Culture 04/2012; 105(2):159-173. · 3.09 Impact Factor
ABSTRACT: Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a range of pathogens
and insect pests. Consequently, NBS-encoding genes have been the focus of a number of recent studies in molecular disease
resistance breeding programs. However, little is known about NBS-encoding genes in Lotus japonicus. In this study, a full set of disease resistance (R) candidate genes encoding NBS from the complete genome of L. japonicus was identified and characterized using structural diversity, chromosomal locations, conserved protein motifs, gene duplications,
and phylogenetic relationships. Distinguished by N-terminal motifs and leucine-rich repeat motifs (LRRs), 92 regular NBS genes
of 158 NBS-coding sequences were classified into seven types: CC-NBS-LRR, TIR-NBS-LRR, NBS-LRR, CC-NBS, TIR-NBS, NBS, and
NBS-TIR. Phylogenetic reconstruction of NBS-coding sequences revealed many NBS gene lineages, dissimilar from results for
Arabidopsis but similar to results from research on rice. Conserved motif structures were also analyzed to clarify their distribution
in NBS-encoding gene sequences. Moreover, analysis of the physical locations and duplications of NBS genes showed that gene
duplication events of disease resistance genes were lower in L. japonicus than in rice and Arabidopsis, which may contribute to the relatively fewer NBS genes in L. japonicus. Sixty-three NBS-encoding genes with clear conserved domain character were selected to check their gene expression levels
by semi-quantitative RT-PCR. The results indicated that 53 of the genes were most likely to be acting as the active genes,
and exogenous application of salicylic acid improved expression of most of the R genes.
-Disease resistance genes-Nucleotide-binding sites-Phylogenetic tree
Plant Systematics and Evolution 04/2012; 289(1):101-110. · 1.34 Impact Factor
ABSTRACT: CCCH-type zinc finger proteins comprise a large protein family. Increasing evidence suggests that members of this family are RNA-binding proteins with regulatory functions in mRNA processing. Compared with those in animals, functions of CCCH-type zinc finger proteins involved in plant growth and development are poorly understood.
Here, we performed a genome-wide survey of CCCH-type zinc finger genes in maize (Zea mays L.) by describing the gene structure, phylogenetic relationships and chromosomal location of each family member. Promoter sequences and expression profiles of putative stress-responsive members were also investigated. A total of 68 CCCH genes (ZmC3H1-68) were identified in maize and divided into seven groups by phylogenetic analysis. These 68 genes were found to be unevenly distributed on 10 chromosomes with 15 segmental duplication events, suggesting that segmental duplication played a major role in expansion of the maize CCCH family. The Ka/Ks ratios suggested that the duplicated genes of the CCCH family mainly experienced purifying selection with limited functional divergence after duplication events. Twelve maize CCCH genes grouped with other known stress-responsive genes from Arabidopsis were found to contain putative stress-responsive cis-elements in their promoter regions. Seven of these genes chosen for further quantitative real-time PCR analysis showed differential expression patterns among five representative maize tissues and over time in response to abscisic acid and drought treatments.
The results presented in this study provide basic information on maize CCCH proteins and form the foundation for future functional studies of these proteins, especially for those members of which may play important roles in response to abiotic stresses.
PLoS ONE 01/2012; 7(7):e40120. · 4.09 Impact Factor
ABSTRACT: Members of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.).
In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution.
Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.
PLoS ONE 01/2011; 6(12):e28488. · 4.09 Impact Factor
ABSTRACT: BURP domain-containing genes comprise a large plant-specific family, yet the functions are very poorly understood, especially in maize (Zea mays) and sorghum (Sorghum vulgare). In this study, 26 BURP family genes in maize (ZmBURP01-15) and sorghum (SbBURP01-11) were identified including the gene structure, phylogenetic relationship, conserved protein motifs and chromosome locations. These genes have diverse exon-intron structures and distinct organization of putative motifs. The distributions of the genes vary: 15 ZmBURP genes are located in maize on five chromosomes, and 11 SbBURP genes in sorghum are on six chromosomes. Based on the phylogenetic analysis of BURP protein sequences from maize, sorghum and other plants, the BURP genes in maize and sorghum were categorized into five subfamilies (RD22-like, PG1β-like, BURP VI, BURP VII and BURP VIII). Transcript level analysis of ZmBURP genes revealed the expression patterns of BURP genes in maize under diffferent stress conditions. The results suggested that only eight ZmBURP genes were responsive to at least one of the stress treatments applied. Among these genes, seven genes (ZmBURP04, ZmBURP05, ZmBURP08, ZmBURP09, ZmBURP12, ZmBURP14, ZmBURP15) were responsive to ABA and cold respectively, two genes (ZmBURP06 and ZmBURP14) were responsive to NaCl. The results presented here provide useful information for further functional analysis of the BURP gene family in maize and sorghum.
Molecular Biology Reports 12/2010; 38(7):4553-63. · 2.93 Impact Factor
ABSTRACT: A large set of candidate nucleotide-binding site (NBS)-encoding genes related to disease resistance was identified in the sorghum (Sorghum bicolor) genome. These resistance (R) genes were characterized based on their structural diversity, physical chromosomal location and phylogenetic relationships. Based on their N-terminal motifs and leucine-rich repeats (LRR), 50 non-regular NBS genes and 224 regular NBS genes were identified in 274 candidate NBS genes. The regular NBS genes were classified into ten types: CNL, CN, CNLX, CNX, CNXL, CXN, NX, N, NL and NLX. The vast majority (97%) of NBS genes occurred in gene clusters, indicating extensive gene duplication in the evolution of S. bicolor NBS genes. Analysis of the S. bicolor NBS phylogenetic tree revealed two major clades. Most NBS genes were located at the distal tip of the long arms of the ten sorghum chromosomes, a pattern significantly different from rice and Arabidopsis, the NBS genes of which have a random chromosomal distribution.
Genetics and Molecular Biology 04/2010; 33(2):292-7. · 0.63 Impact Factor