Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus

Xie, Tongxin; Zeng, Lei; Chen, Xin; Rong, Hao; Wu, Jingjing; Batley, Jacqueline; Jiang, Jinjin; Wang, Youping

doi:10.3390/genes11030280

Cited by 17 publications

(17 citation statements)

References 59 publications

(66 reference statements)

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“…The cis -acting elements in the promoter regions of genes are closely related to the expression pattern of genes ( Chow et al, 2018 ). In addition, the same regulatory elements in gene promoters suggest that they may have similar regulation functions ( Xie et al, 2020 ). Light responsive related elements are most common in all SHI/STYs promoters, indicating that light signals may be involved in S HI/STYs regulating the growth and development of the Brassica species.…”

Section: Discussionmentioning

confidence: 99%

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

et al. 2022

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The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein–protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

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Section: Discussionmentioning

confidence: 99%

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

et al. 2022

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“…The intron-exon organizations were analyzed with the TBtools software [34]. The conserved motifs were detected through the MEME server v5.0.4, with a maximum number of 20 motifs and motif length between 5 wide and 200 wide amino acids [37]. The phylogenetic tree, motifs and gene structures were visualized using the TBtools software.…”

Section: Duplication Events Orthologous Groups Conserved Motifs and Gene Structure Analysesmentioning

confidence: 99%

Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

Huang

Zhang

et al. 2021

IJMS

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The GLABROUS1 enhancer-binding protein (GeBP) gene family encodes a typical transcription factor containing a noncanonical Leucine (Leu-)-zipper motif that plays an essential role in regulating plant growth and development, as well as responding to various stresses. However, limited information on the GeBP gene family is available in the case of the Gramineae crops. Here, 125 GeBP genes from nine Gramineae crops species were phylogenetically classified into four clades using bioinformatics analysis. Evolutionary analyses showed that whole genome duplication (WGD) and segmental duplication play important roles in the expansion of the GeBP gene family. The various gene structures and protein motifs revealed that the GeBP genes play diverse functions in plants. In addition, the expression profile analysis of the GeBP genes showed that 13 genes expressed in all tested organs and stages of development in rice, with especially high levels of expression in the leaf, palea, and lemma. Furthermore, the hormone- and metal-induced expression patterns showed that the expression levels of most genes were affected by various biotic stresses, implying that the GeBP genes had an important function in response to various biotic stresses. Furthermore, we confirmed that OsGeBP11 and OsGeBP12 were localized to the nucleus through transient expression in the rice protoplast, indicating that GeBPs function as transcription factors to regulate the expression of downstream genes. This study provides a comprehensive understanding of the origin and evolutionary history of the GeBP genes family in Gramineae, and will be helpful in a further functional characterization of the GeBP genes.

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“…Other gene families in rapeseed have also experienced a WGD/segmental duplication event, including 73.81% BnLBDs , 92.3% BnKCSs , 70.98% BnNPFs , 96.96% BnATGs , and 73.4% BnMATEs . Thus, WGD/segmental duplication is a main force for gene family expansion in rapeseed [ 66 , 91 , 92 , 93 , 94 ]. However, not all the duplicated genes were retained; some genes were quickly erased to maintain the genome stability [ 95 ].…”

Section: Discussionmentioning

confidence: 99%

“…Eleven Arabidopsis B-ARRs were obtained from TAIR ( , accessed on 7 June 2022). The phylogenetic tree of B-ARRs in A. thaliana , B. rapa , B. oleracea , and B. napus was constructed with the neighbor-joining of MEGA 7.0 ( , accessed on 7 June 2022), using the parameters as Xie et al [ 65 , 66 ]. The gene structure of BnARRs were obtained from the genome data of B. napus ( , accessed on 5 June 2022) [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus

Jiang

Chen

et al. 2022

Genes

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The type-B authentic response regulators (type-B ARRs) are positive regulators of cytokinin signaling and involved in plant growth and stress responses. In this study, we used bioinformatics, RNA-seq, and qPCR to study the phylogenetic and expression pattern of 35 type-B ARRs in Brassica napus. The BnARRs experienced gene expansion and loss during genome polyploidization and were classified into seven groups. Whole-genome duplication (WGD) and segmental duplication were the main forces driving type-B ARR expansion in B. napus. Several BnARRs with specific expression patterns during rapeseed development were identified, including BnARR12/14/18/23/33. Moreover, we found the type-B BnARRs were involved in rapeseed development and stress responses, through participating in cytokinin and ABA signaling pathways. This study revealed the origin, evolutionary history, and expression pattern of type-B ARRs in B. napus and will be helpful to the functional characterization of BnARRs.

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Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus

Cited by 17 publications

References 59 publications

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops

Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus

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