Genome-wide analysis and expression profiles of glyoxalase gene families in Chinese cabbage (Brassica rapa L)

Abstract Background In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few of B3 transcription factors are reported to regulate embryogenesis, little is known about the possible roles of B3 superfamily during SE especially in citrus. Results In this study, a total of 72 (CsB3) and 69 (CgB3) putative B3 superfamily members were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively, each comprised four gene families and 14 phylogenetic classes. The B3 genes were unevenly distributed over citrus chromosomes and other non-anchored scaffolds. Genome duplication analysis indicated that the segmental and tandem duplication events have significantly contributed to the expansion of the citrus B3 superfamily. The evolutionary relationships among the B3 family members and their putative functions were deduced based on the results of phylogenetic analysis. Furthermore, transcriptomic analysis showed that citrus B3 genes have differential expression levels in various tissues, suggesting distinct biological roles of different members. Expression analysis revealed that the B3 superfamily members showed four types of expression profiles during SE in citrus and may play functional roles during SE, especially at late SE stages. Of them, CsARF19 is specifically expressed in sweet orange and at markedly higher levels in the embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions This study provides a genome-wide analysis of citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, which contributes to a better understanding of the B3 genes in citrus and their association with SE.

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Genome-wide gene expression profiles in response to downy mildew in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

European Journal of Plant Pathology ◽

10.1007/s10658-018-1427-6 ◽

2018 ◽

Vol 151 (4) ◽

pp. 861-873 ◽

Cited By ~ 2

Author(s):

Jingjuan Li ◽

Qian Ding ◽

Fengde Wang ◽

Huayin Li ◽

Yihui Zhang ◽

...

Keyword(s):

Gene Expression ◽

Downy Mildew ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Genome Wide ◽

Genome Wide Gene Expression

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Genome-wide analysis of the R2R3-MYB transcription factor genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals their stress and hormone responsive patterns

BMC Genomics ◽

10.1186/s12864-015-1216-y ◽

2015 ◽

Vol 16 (1) ◽

pp. 17 ◽

Cited By ~ 36

Author(s):

Zhen Wang ◽

Jun Tang ◽

Rong Hu ◽

Peng Wu ◽

Xi-Lin Hou ◽

...

Keyword(s):

Transcription Factor ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Myb Transcription Factor ◽

Genome Wide Analysis ◽

Genome Wide ◽

Transcription Factor Genes ◽

R2r3 Myb

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Genome‐wide analysis of the callose enzyme families of fertile and sterile flower buds of the Chinese cabbage ( Brassica rapa L. ssp. pekinensis )

FEBS Open Bio ◽

10.1002/2211-5463.12685 ◽

2019 ◽

Vol 9 (8) ◽

pp. 1432-1449

Author(s):

Yanan Pu ◽

Lingyun Hou ◽

Yingqi Guo ◽

Ikram Ullah ◽

Yongping Yang ◽

...

Keyword(s):

Brassica Rapa ◽

Chinese Cabbage ◽

Flower Buds ◽

Genome Wide Analysis ◽

Genome Wide ◽

Enzyme Families

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Genome-wide analysis of the SBP-box gene family in Chinese cabbage (Brassica rapa subsp. pekinensis)

Genome ◽

10.1139/gen-2015-0074 ◽

2015 ◽

Vol 58 (11) ◽

pp. 463-477 ◽

Cited By ~ 14

Author(s):

Hua-Wei Tan ◽

Xiao-Ming Song ◽

Wei-Ke Duan ◽

Yan Wang ◽

Xi-Lin Hou

Keyword(s):

Gene Family ◽

Brassica Rapa ◽

Plant Development ◽

Chinese Cabbage ◽

Interaction Network ◽

Pcr Analysis ◽

Genome Wide Analysis ◽

Genome Wide ◽

Transcription Factor Genes ◽

Gene Duplication And Loss

The SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box gene family contains highly conserved plant-specific transcription factors that play an important role in plant development, especially in flowering. Chinese cabbage (Brassica rapa subsp. pekinensis) is a leafy vegetable grown worldwide and is used as a model crop for research in genome duplication. The present study aimed to characterize the SBP-box transcription factor genes in Chinese cabbage. Twenty-nine SBP-box genes were identified in the Chinese cabbage genome and classified into six groups. We identified 23 orthologous and 5 co-orthologous SBP-box gene pairs between Chines cabbage and Arabidopsis. An interaction network among these genes was constructed. Sixteen SBP-box genes were expressed more abundantly in flowers than in other tissues, suggesting their involvement in flowering. We show that the MiR156/157 family members may regulate the coding regions or 3′-UTR regions of Chinese cabbage SBP-box genes. As SBP-box genes were found to potentially participate in some plant development pathways, quantitative real-time PCR analysis was performed and showed that Chinese cabbage SBP-box genes were also sensitive to the exogenous hormones methyl jasmonic acid and salicylic acid. The SBP-box genes have undergone gene duplication and loss, evolving a more refined regulation for diverse stimulation in plant tissues. Our comprehensive genome-wide analysis provides insights into the SBP-box gene family of Chinese cabbage.

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Genome-Wide Analysis of nsLTP Gene Family and Identification of SiLTPs Contributing to High Oil Accumulation in Sesame (Sesamum indicum L.)

International Journal of Molecular Sciences ◽

10.3390/ijms22105291 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5291

Author(s):

Shengnan Song ◽

Jun You ◽

Lisong Shi ◽

Chen Sheng ◽

Wangyi Zhou ◽

...

Keyword(s):

Oil Content ◽

Expression Profiles ◽

Gene Families ◽

Sesamum Indicum ◽

Lipid Transfer ◽

Oil Accumulation ◽

Specific Expression ◽

Sesame Seeds ◽

Genome Wide Analysis ◽

Genome Wide

The biosynthesis and storage of lipids in oil crop seeds involve many gene families, such as nonspecific lipid-transfer proteins (nsLTPs). nsLTPs are cysteine-rich small basic proteins essential for plant development and survival. However, in sesame, information related to nsLTPs was limited. Thus, the objectives of this study were to identify the Sesamum indicum nsLTPs (SiLTPs) and reveal their potential role in oil accumulation in sesame seeds. Genome-wide analysis revealed 52 SiLTPs, nonrandomly distributed on 10 chromosomes in the sesame variety Zhongzhi 13. Following recent classification methods, the SiLTPs were divided into nine types, among which types I and XI were the dominants. We found that the SiLTPs could interact with several transcription factors, including APETALA2 (AP2), DNA binding with one finger (Dof), etc. Transcriptome analysis showed a tissue-specific expression of some SiLTP genes. By integrating the SiLTPs expression profiles and the weighted gene co-expression network analysis (WGCNA) results of two contrasting oil content sesame varieties, we identified SiLTPI.23 and SiLTPI.28 as the candidate genes for high oil content in sesame seeds. The presumed functions of the candidate gene were validated through overexpression of SiLTPI.23 in Arabidopsis thaliana. These findings expand our knowledge on nsLTPs in sesame and provide resources for functional studies and genetic improvement of oil content in sesame seeds.

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