Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of TLC Genes in Maize

Si, Weina; Hang, Tianlu; Guo, Mingyue; Chen, Zhe; Liang, Qizhi; Gu, Longjiang; Ding, Tao

doi:10.3390/ijms20215484

Cited by 16 publications

(12 citation statements)

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“…Gene duplications are an essential mechanism for creating genetic novelty in all plants, which could help organisms to adapt to environmental change (Alvarez-Buylla et al, 2000;Kondrashov, 2012). There are different kind of gene duplication, including TD, PD, DSD, WGD, and TD, which differentially contribute to the expansion of plantspecific genes (Qiao et al, 2018(Qiao et al, , 2019Si et al, 2019). The analysis of the MYB genes in Setaria italica (Muthamilarasan et al, 2014), AP2/ERF and WRKY genes in grapes (Guo et al, 2014), SWEET, and F-box genes in Chinese pear showed that whole-genome/ segmental and tandem duplications contributed to the gene family expansion (Li, Qin, et al, 2017;Wang, Yin, et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

Manzoor

Abdullah

et al. 2021

Physiologia Plantarum

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The Multidrug and Toxic Compound Extrusion (MATE) protein belongs to a secondary transporter gene family, which plays a primary role in transporting many kinds of substrates such as organic compounds, secondary metabolites, and phytohormones. MATE protein members exist in both prokaryotes and eukaryotes. However, evolution and comprehensive analysis of the MATE genes has not been performed in Rosaceae species. In the present study, a total of 404 MATEs genes were identified from six Rosaceae genomes (Prunus avium, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Prunus mume, and Malus domestica) and classified into eight main subfamilies (I-VII) based on structural and phylogenetic analysis. Microcollinearity analysis showed that whole-genome duplication events might play a vital role in the expansion of the MATE genes family. The Ka/Ks analysis, chromosomal localization, subcellular localization, and molecular characteristics (length, weight, and pI) were performed using various bioinformatics tools. Furthermore, different subfamilies have different introns-exons structures, cis-acting elements, and conserved motifs analysis, indicating functional divergence in the MATE family. Subsequently, RNA-seq analysis and real-time qRT-PCR were conducted during Chinese pear fruit development.Moreover, PbMATE genes were significantly expressed under hormonal treatments of MeJA (methyl jasmonate), SA (salicylic acid), and ABA (abscisic acid). Overall, our results provide helpful insights into the functions, expansion complexity, and evolutions of the MATE genes in Chinese pear and five Rosaceae species.

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Section: Discussionmentioning

confidence: 99%

Genome‐wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

Manzoor

Abdullah

et al. 2021

Physiologia Plantarum

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“…Based on their positions in the genome annotations, the chromosomal distributions of the maize SOD genes were displayed from top to bottom on the chromosomes using the MapInspect software. Gene duplication analysis of ZmSODs was performed according to previous study ( Si et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses

Liu

Shang

et al. 2021

Genet. Mol. Biol.

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Superoxide dismutase proteins (SODs) are antioxidant enzymes with important roles in abiotic stress responses. The SOD gene family has been systematically analyzed in many plants; however, it is still poorly understood in maize. Here, a bioinformatics analysis of maize SOD gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, gene duplications, promoter cis -elements and GO annotations. In total, 13 SOD genes were identified in maize and five members were involved in segmental duplication. Phylogenetic analysis indicated that SODs from maize and other plants comprised two groups, which could be further classified into different subgroups, with most members in the same subgroup having the same subcellular localization. The ZmSOD promoters contained 2-10 stress-responsive cis -elements with different distributions. Heatmap analysis indicated that ZmSODs were expressed in most of the detected tissues and organs. The expression patterns of ZmSODs were investigated under drought and salt treatments by qRT-PCR, and most members were responsive to drought or salt stress, especially some ZmSODs with significant expression changes were identified, such as ZmCSD2 and ZmMSD2 , suggesting the important roles of ZmSODs in abiotic stress responses. Our results provide an important basis for further functional study of ZmSODs in future study.

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“…Gene duplication events (TD, PD, WGD, DSS, and TRD) of the GAox family were revealed in three Rosaceae species ( P. avium , Fragaria vesca , and P. mume ) to help researchers better understand gene evolution and novel functions. Five types of duplications (dispersed duplication (DSD), tandem duplication (TD), proximal duplication (PD), whole-genome duplication (WGD), and (TRD) transposed duplication) were investigated in the GAox gene family, all of which contribute to the proliferation of certain genes in plants in diverse ways ( Si et al, 2019 ). Tandem and whole-genome duplications played a vital role in gene family expansion like in Vitis vinifera (grape) ( Guo et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress

et al. 2022

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The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus avium L., F. vesca, and P. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the PavGAox genes have a remarkably well-maintained exon–intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation, PavGAox genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in Prunus avium L., F. vesca, and P. mume revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of cis-regulatory elements in the upstream region of the 140 PavGAox members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the PavGAox genes display a variety of tissue expression patterns in diverse tissues, with most of the PavGAox genes displaying tissue-specific expression patterns. Furthermore, most of the PavGAox genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of PavGAox genes are responsible for maintaining the GA level in plant-like Pav co4017001.1 g010.1.br, Pav sc0000024.1 g340.1.br, and Pav sc0000024.1 g270.1.mk. The subcellular localization of PavGAox protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family’s interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.

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Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of TLC Genes in Maize

Cited by 16 publications

References 58 publications

Genome‐wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

Genome‐wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses

Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress

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