Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants

Xie, Jianbo; Li, Ying; Liu, Xiaomin; Zhao, Yiyang; Li, Bai-Lian; Ingvarsson, Pär K.; Zhang, Deqiang

doi:10.1105/tpc.18.00601

Cited by 40 publications

(55 citation statements)

References 59 publications

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“…a similar function in pepper. However, CabHLHs that were not expressed in any tissues (such as CabHLH23, CabHLH85, CabHLH39, CabHLH105, and CabHLH108) may have lost their functions during evolution and become pseudogenes, as has been demonstrated in the evolution of other plant genomes (Innan and Kondrashov, 2010;Xie et al, 2019). In addition, several duplicated pairs (such as CabHLH34/CabHLH58 and CabHLH8/CabHLH17) had significantly different expression patterns, indicating that functional diversification of duplicated CabHLH pairs had occurred during the course of evolution (Blanc and Wolfe, 2004).…”

Section: Discussionmentioning

confidence: 94%

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

Zhang

Chen²,

Liang³

et al. 2020

Front. Genet.

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Plant basic helix-loop-helix (bHLH) transcription factors are involved in the regulation of various biological processes in plant growth, development, and stress response. However, members of this important transcription factor family have not been systematically identified and analyzed in pepper (Capsicum annuum L.). In this study, we identified 122 CabHLH genes in the pepper genome and renamed them based on their chromosomal locations. CabHLHs were divided into 21 subfamilies according to their phylogenetic relationships, and genes from the same subfamily had similar motif compositions and gene structures. Sixteen pairs of tandem and segmental duplicated genes were detected in the CabHLH family. Cis-elements identification and expression analysis of the CabHLHs revealed that they may be involved in plant development and stress responses. This study is the first comprehensive analysis of the CabHLH genes and will serve as a reference for further characterization of their molecular functions.

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Section: Discussionmentioning

confidence: 94%

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

Zhang

Chen²,

Liang³

et al. 2020

Front. Genet.

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“…Whether those sequences are of functional importance remains an open question. In some cases, pseudogenes contribute, for example, transcription factor binding sites for noncoding RNA expression (Xie et al, 2019).…”

Section: Researchmentioning

confidence: 99%

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

et al. 2019

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Summary Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine‐tuning important traits is of great importance. MADS‐box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC‐type MADS‐box genes. Homoeolog retention is significantly above the average genome‐wide retention rate for wheat genes, indicating that many MIKC‐type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily‐specific expression pattern, indicating broad conservation of function of MIKC‐type genes during wheat evolution. We also found extensive expansion of some MIKC‐type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC‐type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC‐type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.

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“…In addition, we found five ADH genes with no or few instances of expression compared to their paralogous genes in all investigated pear tissues, suggesting that these five ADH genes (Pbr024187.1, Pbr004679.1, Pbr003626.1, Pbr040240.1, and Pbr040236.1) may haveundergone nonfunctionalization or pseudogenization. This result provides evidence for the hypothesis that two gene copies derived via gene duplication may evolve toward distinct evolutionary fates, with one of the two copies gradually losing function and undergoing pseudogenization [59].…”

Section: Transcriptome Expression Profiles and Qrt-pcr Analysis Of Admentioning

confidence: 69%

Recurrent single-gene duplication drives the expansion and expression diversification of the ADH gene family in pear and other Rosaceae species

Zhang¹,

Zeng²,

Qiao³

et al. 2019

Preprint

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Background Alcohol dehydrogenases (ADHs) are essential to plant growth and the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Chinese white pear ( Pyrus bretschneideri ) and other fruit species from the family Rosaceae.Results In this study, 464 ADH genes were identified in eight Rosaceae fruit species and 68 of the genes were from pear. Based on the analyses of phylogeny and conserved motifs, the pear ADH genes were classified into four subgroups (I, II, III, and IV). The chromosomal distribution of the genes was found to be uneven and numerous clusters of physically linked ADH genes were detected. Frequent single-gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those that derived from other types of duplication. RNA-sequencing and quantitative-real time-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds that are found during fruit development.Conclusion Comprehensive analyses were conducted in eight Rosaceae species and 464 ADH genes were identified. The results of this study provide new insights into the evolution and expression characteristics of ADH family genes in pear and other Rosaceae species.

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Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants

Cited by 40 publications

References 59 publications

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Recurrent single-gene duplication drives the expansion and expression diversification of the ADH gene family in pear and other Rosaceae species

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