Genome-Wide Identification of YABBY Genes in Orchidaceae and Their Expression Patterns in Phalaenopsis Orchid

The plant YABBY transcription factors are key regulators in the lamina development of lateral organs. Orchid is one of the largest families in angiosperm and known for their unique floral morphology, reproductive biology, and diversified lifestyles. However, nothing is known about the role of YABBY genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 YABBY genes, including 15 genes in CRC/DL, eight in INO, 17 in YAB2, and 14 in FIL clade, were identified from the eight orchid species. A sequence analysis showed that all protein sequences encoded by these YABBY genes share the highly conserved C2C2 zinc-finger domain and YABBY domain (a helix-loop-helix motif). A gene structure analysis showed that the number of exons is highly conserved in the same clades. The genes in YAB2 clade have six exons, and genes in CRC/DL, INO, and FIL have six or seven exons. A phylogenetic analysis showed all 54 orchid YABBY genes could be classified into four major clades, including CRC/DL, INO, FIL, and YAB2. Many of orchid species maintain more than one member in CRC/DL, FIL, and YAB2 clades, implying functional differentiation among these genes, which is supported by sequence diversification and differential expression. An expression analysis of PhalaenopsisYABBY genes revealed that members in the CRC/DL clade have concentrated expressions in the early floral development stage and gynostemium, the fused male and female reproductive organs. The expression of PeINO is consistent with the biological role it played in ovule integument morphogenesis. Transcripts of members in the FIL clade could be obviously detected at the early developmental stage of the flowers. The expression of three genes, PeYAB2,PeYAB3, and PeYAB4, in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and PeYAB4 was transcribed at a relatively higher level than that of PeYAB2 and PeYAB3. Together, this comprehensive analysis provides the basic information for understanding the function of the YABBY gene in Orchidaceae.

Download Full-text

Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

PeerJ ◽

10.7717/peerj.11780 ◽

2021 ◽

Vol 9 ◽

pp. e11780

Author(s):

Ruifang Ma ◽

Bin Huang ◽

Zhinuo Huang ◽

Zhijun Zhang

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Moso Bamboo ◽

Lateral Organs ◽

Genome Wide ◽

Yabby Gene ◽

Resistance To Stress ◽

Hormone Responses ◽

High Level

Background The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo. Methods In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments. Results Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.

Download Full-text

Genome-wide identification and characterization of the ALOG gene family in Petunia

BMC Plant Biology ◽

10.1186/s12870-019-2127-x ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Feng Chen ◽

Qin Zhou ◽

Lan Wu ◽

Fei Li ◽

Baojun Liu ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Functional Characterization ◽

Reproductive Organs ◽

Genome Wide ◽

Domain Of Unknown Function ◽

Intron Structure ◽

Identification And Characterization ◽

Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

Download Full-text

Genome-Wide Identification of the YABBY Gene Family in Seven Species of Magnoliids and Expression Analysis in Litsea

Plants ◽

10.3390/plants10010021 ◽

2020 ◽

Vol 10 (1) ◽

pp. 21

Author(s):

Xuedie Liu ◽

Xing-Yu Liao ◽

Yu Zheng ◽

Meng-Jia Zhu ◽

Xia Yu ◽

...

Keyword(s):

Gene Family ◽

Developmental Stages ◽

Gene Family Evolution ◽

Protein Structure Analysis ◽

Reading Frame ◽

Lateral Organs ◽

Genome Wide ◽

Spatial Level ◽

Yabby Gene ◽

The Common

The YABBY gene family, specific to seed plants, encodes a class of transcription factors in the lamina maintenance and development of lateral organs. Magnoliids are sisters to the clade-containing eudicots and monocots, which have rapidly diversified among the common ancestors of these three lineages. However, prior to this study, information on the function of the YABBY genes in magnoliids was extremely limited to the third major clades and the early diverging lineage of Mesangiospermae. In this study, the sum of 55 YABBY genes including five genes in INO, six in CRC, eight in YAB2, 22 in YAB5, and 14 in FIL clade were identified from seven magnoliid plants. Sequence analysis showed that all encoded YABBY protein sequences possess the highly conserved YABBY domain and C2C2 zinc-finger domain. Gene and protein structure analysis indicates that a certain number of exons were highly conserved and similar in the same class, and YABBY genes encode proteins of 71–392 amino acids and an open reading frame of 216–1179 bp in magnoliids. Additionally, the predicted molecular weight and isoelectric point of YABBY proteins in three species ranged from 7689.93 to 43578.13 and from 5.33 to 9.87, respectively. Meanwhile, the YABBY gene homolog expression of Litsea was detected at a temporal and spatial level during various developmental stages of leaf and reproductive tissues. This research could provide a brief overview of YABBY gene family evolution and its differential expression in magnoliids. Therefore, this comprehensive diversification analysis would provide a new insight into further understanding of the function of genes in seven magnoliids.

Download Full-text

Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus

International Journal of Molecular Sciences ◽

10.3390/ijms22179651 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9651

Author(s):

Mingxing Cheng ◽

Huanran Yuan ◽

Ruihua Wang ◽

Jianing Zou ◽

Ting Liang ◽

...

Keyword(s):

Metal Binding ◽

Tandem Duplication ◽

Expression Patterns ◽

Functional Differentiation ◽

Chromosome 12 ◽

Genome Wide ◽

Strong Negative Selection ◽

Duplication Events ◽

Ks Values ◽

Promoter Activity Assay

Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl2, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.

Download Full-text

Genome-wide identification and analyses of bHLH family genes in Brassica napus

Canadian Journal of Plant Science ◽

10.1139/cjps-2018-0230 ◽

2019 ◽

Vol 99 (5) ◽

pp. 589-598 ◽

Cited By ~ 3

Author(s):

Wei Shen ◽

Xin Cui ◽

Hui Li ◽

Rui-Min Teng ◽

Yong-Xin Wang ◽

...

Keyword(s):

Brassica Napus ◽

Expression Patterns ◽

Genomic Analysis ◽

Comparative Genomic ◽

Oilseed Crop ◽

Plant Growth And Development ◽

The Third ◽

Helix Loop Helix ◽

Genome Wide ◽

Binding Type

The bHLH (basic/helix-loop-helix) protein is one of the largest transcription factors (TFs) that is essential in regulating plant growth and development. Although the bHLH family has been identified in some organisms, a systemic study has not been performed in Brassica napus, which is the third most important oilseed crop worldwide. In the present study, a total of 460 bHLH TFs were identified from the genome of B. napus and clustered into 25 subfamilies. Structural analysis was used to identify the DNA binding type and conserved amino residues of the identified sequence in the bHLH domain. In addition, a comparative genomic analysis of B. napus and its progenitors (Brassica rapa and Brassica oleracea) and two basal angiosperms (Amborella trichopoda and Vitis vinifera) was performed to trace the change during expansion and evolution of the bHLH family. The bHLH TFs in leaves and roots showed various expression patterns. The homologs of the AA-subgenome and CC-subgenome exhibited similar expression patterns, but were more divergent between the homologs caused from other duplicate events.

Download Full-text

Genome-wide identification of the tea plant bHLH transcription factor family and discovery of candidate regulators of trichome formation

Scientific Reports ◽

10.1038/s41598-021-90205-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Renjian Liu ◽

Yuyuan Wang ◽

Song Tang ◽

Jiarong Cai ◽

Shaoqun Liu ◽

...

Keyword(s):

Transcriptional Activation ◽

Expression Patterns ◽

Tea Plant ◽

Bhlh Transcription Factor ◽

Phylogenetic Tree Analysis ◽

Helix Loop Helix ◽

Trichome Formation ◽

Genome Wide ◽

Tea Plants ◽

Bhlh Transcription Factors

AbstractLeaf trichomes play vital roles in plant resistance and the quality of tea. Basic helix-loop-helix (bHLH) transcription factors (TFs) play an important role in regulating plant development and growth. In this study, a total of 134 CsbHLH proteins were identified in the Camellia sinensis var. sinensis (CSS) genome. They were divided into 17 subgroups according to the Arabidopsis thaliana classification. Phylogenetic tree analysis indicated that members of subgroups IIIc-I and IIIc-II might be associated with trichome formation. The expression patterns of CsbHLH116, CsbHLH133, CsbHLH060, CsbHLH028, CsbHLH024, CsbHLH112 and CsbHLH053 from clusters 1, 3 and 5 were similar to the trichome distribution in tea plants. CsbHLH024 and CsbHLH133 were located in the cell nucleus and possessed transcriptional activation ability. They could interact with CsTTG1, which is a regulator of tea trichome formation. This study provides useful information for further research on the function of CsbHLHs in trichome formation.

Download Full-text

Genome-wide analysis of OVATE family proteins in cucumber (Cucumis sativus L.)

10.21203/rs.2.18804/v1 ◽

2019 ◽

Author(s):

Lijie Han ◽

Xiaofei Song ◽

Zhongyi Wang ◽

Xiaofeng Liu ◽

Liying Yan ◽

...

Keyword(s):

Cucumis Sativus ◽

Expression Patterns ◽

Ectopic Expression ◽

Reproductive Organs ◽

Cucumis Sativus L ◽

Hormone Response Elements ◽

Genome Wide ◽

Cucumber Fruit ◽

Specific Proteins ◽

Gibberellin Treatment

Abstract Background: OVATE family proteins (OFPs) are plant-specific proteins with the conserved OVATE domain that regulating plant growth and development. Although these OFPs have been studied in several species, the biological functions of this OFP gene family remain largely unknown in cucumber (Cucumis sativus L.). Results: In this study, we identified 19 CsOFPs in cucumber. This CsOFPs are distributed on seven chromosomes and can be divided into four subgroups. Most CsOFP genes are expressed in reproductive organs although have different expression patterns. Cis-elements analysis showed that there are six kinds of hormone response elements in CsOFPs and exogenous gibberellin treatment leads to a ‘first increase then decrease’ expression pattern of CsOFP7, CsOFP11 and CsOFP12. Ectopic expression of CsOFP11 in Arabidopsis resulted in shorter and blunt siliques. Conclusions: Together, these results indicated that CsOFPs may play important roles in cucumber fruit development.

Download Full-text

Genome-Wide Identification of Tea Plant bHLH Transcription Factor Family and Discovery of Candidate Regulator for Trichome Formation

10.21203/rs.3.rs-148784/v1 ◽

2021 ◽

Author(s):

Renjian Liu ◽

Yuyuan Wang ◽

Song Tang ◽

Jiarong Cai ◽

Shaoqun Liu ◽

...

Keyword(s):

Transcriptional Activation ◽

Expression Patterns ◽

Tea Plant ◽

Bhlh Transcription Factor ◽

Phylogenetic Tree Analysis ◽

Helix Loop Helix ◽

Trichome Formation ◽

Genome Wide ◽

Tea Plants ◽

Bhlh Transcription Factors

Abstract Leaf trichomes play vital roles in plant resistance and tea quality. Basic helix-loop-helix (bHLH) transcription factors (TFs) play an important role in regulating plant development and growth. However, it is poorly understood whether bHLH TFs are associated with trichome formation in tea plant. In this study, a total of 134 CsbHLH proteins were identified in the Camellia sinensis var. sinensis (CSS) genome. All identified proteins were divided into 19 subgroups according to the Arabidopsis thaliana classification. Phylogenetic tree analysis indicated that the members of group IIIc-I and group IIIc-II might be associated with trichome formation. Expression analysis showed that the candidate genes associated with trichome formation in tea plant were primarily located in cluster 1, cluster 3 and cluster 5. The expression patterns of CsbHLH116, CsbHLH133, CsbHLH060, CsbHLH028, CsbHLH024, CsbHLH112 and CsbHLH053 from these clusters were similar to the trichome distribution in tea plants. Notably, CsbHLH024 and CsbHLH133 were highly expressed in the young tissues of different cultivars. CsbHLH024 and CsbHLH133 possessed transcriptional activation ability and could interact with CsTTG1, a regulator of tea trichome formation. This study provides useful information for further research on the function of CsbHLHs in the regulation of trichome formation.

Download Full-text

Cloning, molecular evolution and functional characterization of ZmbHLHl6, the maize ortholog of OsTIP2 (OsbHLH142)

10.1101/140806 ◽

2017 ◽

Author(s):

Yongming Liu ◽

Jia Li ◽

Gui Wei ◽

Yonghao Sun ◽

Yanli Lu ◽

...

Keyword(s):

Transcription Factor ◽

Expression Patterns ◽

Functional Characterization ◽

Protein A ◽

Reproductive Organs ◽

Male Reproduction ◽

Yeast Cells ◽

Bhlh Transcription Factor ◽

Helix Loop Helix ◽

A Genome

AbstractAbstract Basic helix-loop-helix (bHLH) transcription factors play key roles in plant male reproduction. More than 14 bHLH proteins related to pollen development have been cloned from rice and Arabidopsis. However, little is known about the role of the bHLH family in maize microspore development. In this study, the bHLH transcription factor ZmbHLH16 was cloned. ZmbHLH16 shares high similarity with the OsTIP2 (OsbHLH142) protein, a master regulator of the developmental coordination of male reproduction in rice. Expression characterization analysis showed that ZmbHLH16 is preferentially expressed in male reproductive organs and is located in the nucleus. Through nucleotide variation analysis, 36 polymorphic sites in ZmbHLH16, including 23 SNPs and 13 InDels, were detected among 78 maize inbred lines. Neutrality tests and linkage disequilibrium analysis showed that ZmbHLH16 experienced no significant evolutionary pressure. A yeast one-hybrid experiment showed that the first 80 residues in the N-terminus of ZmbHLH16 had transactivation activity, whereas the full length did not. To identify potential ZmbHLH16 interactors, 395 genes that shared similar expression patterns in a genome-wide search were obtained through coexpression analysis. Among these genes, the transcription factor ZmbHLH51 had an expression pattern and subcellular localization similar to those of ZmbHLH16. The interaction between ZmbHLH51 and ZmbHLH16 was verified in yeast cells. In addition to the typical bHLH domain, other regions of ZmbHLH16 were necessary and adequate for its heterodimerization with ZmbHLH51. Our results contribute to a solid foundation for further understanding the functions and mechanisms of ZmbHLH16.

Download Full-text