Whole‐Genome Sequence of Synthesized Allopolyploids in <i>Cucumis</i> Reveals Insights into the Genome Evolution of Allopolyploidization

Yu, Xiaqing; Wang, Panqiao; Li, Ji; Zhao, Qinzheng; Ji, Changmian; Zhu, Zhanguo; Zhai, Yufei; Qin, Xiaodong; Zhou, Junguo; Yu, Haiyan; Cheng, Xin-Chao; Isshiki, Shiro; Jahn, Molly; Doyle, Jeff J.; Ottosen, Carl‐Otto; Bai, Yuling; Cai, Qinsheng; Cheng, Chunyan; Lou, Qunfeng; Huang, Sanwen; Chen, Jinfeng

doi:10.1002/advs.202004222

Cited by 27 publications

(18 citation statements)

References 123 publications

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“…The reactivation of LTRs (Long Terminal Repeats) in resynthesized hexaploid wheat produces alterations in the expression of neighboring genes [ 303 , 304 ]. Similar results were observed in different species such as synthetic Arabiposis polyploids [ 22 ], synthetic Cucumis polyploids [ 287 ], or Gossypium [ 305 ], among others. TEs can also experience an increase in copy number following the hybridization, as it has been reported in tobacco [ 306 ] or Brassica [ 307 ].…”

Section: Readjustments Of the Merged Genomessupporting

confidence: 83%

“…For example, in the new synthetic allopolyploid Cucumis sativus × C. hystryx drastic changes at genomic level emerge rapidly after hybridization, while others occur in later generations at a slower rate. The study has revealed that the C. sativum subgenome is dominant, preserving more sequences and showing a higher expression level than the C. hystryx genome [ 287 ]. However, in tetraploid cotton, downregulation of the homoeologous gene copies of the submissive genome is mediated by both, cis- and trans-regulatory elements from the dominant genome [ 288 ].…”

Section: Readjustments Of the Merged Genomesmentioning

confidence: 99%

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Genomic and Meiotic Changes Accompanying Polyploidization

Blasio

Prieto

Pradillo

et al. 2022

Plants

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Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.

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Section: Readjustments Of the Merged Genomessupporting

confidence: 83%

Section: Readjustments Of the Merged Genomesmentioning

confidence: 99%

Genomic and Meiotic Changes Accompanying Polyploidization

Blasio

Prieto

Pradillo

et al. 2022

Plants

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“…Gene expression was affected by the number and distance of nearby TEs [ 56 ]. The subgenome with the greatest TE density had a relatively high probability of gene loss and inactivation and a weak overall expression level [ 57 ]. The number of TEs in B. oleracea was slightly greater than that in B. rapa , which may also provide an explanation for the bias of MBD gene expression in B. napus .…”

Section: Discussionmentioning

confidence: 99%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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Background Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis. Results In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus. Conclusions In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

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“…Therefore, the acquisition of high-throughput markers is the key to comprehensively evaluate REs in the overall genome in Populus . Recently, using genome sequencing and high-precision polyploid genome assembly ( Zhou et al, 2020 ; Yu et al, 2021 ) provides technical support for the acquisition of high-throughput SNPs, which is expected to solve the problem.…”

Section: Discussionmentioning

confidence: 99%

High-Frequency Homologous Recombination Occurred Preferentially in Populus

et al. 2021

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Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.

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Whole‐Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization

Cited by 27 publications

References 123 publications

Genomic and Meiotic Changes Accompanying Polyploidization

Genomic and Meiotic Changes Accompanying Polyploidization

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

High-Frequency Homologous Recombination Occurred Preferentially in Populus

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