Abstract
The importance of allopolyploidy in plant evolution has been widely recognized. The genetic changes triggered by allopolyploidy, however, are not yet fully understood due to inconsistent phenomena reported across diverse species. The construction of synthetic polyploids offers a controlled approach to systematically reveal genomic changes that occur during the process of polyploidy. This study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, with high‐quality assembly. The two subgenomes are confidently partitioned and the C. sativus‐originated subgenome predominates over the C. hystrix‐originated subgenome, retaining more sequences and showing higher homeologous gene expression. Most of the genomic changes emerge immediately after interspecific hybridization. Analysis of a series of genome sequences from several generations (S0, S4–S13) of C. ×hytivus confirms that genomic changes occurred in the very first generations, subsequently slowing down as the process of diploidization is initiated. The duplicated genome of the allopolyploid with double genes from both parents broadens the genetic base of C. ×hytivus, resulting in enhanced phenotypic plasticity. This study provides novel insights into plant polyploid genome evolution and demonstrates a promising strategy for the development of a wide array of novel plant species and varieties through artificial polyploidization.
Highlights
Polyploids are organisms that contain three or more sets of chromosomes
By aligning all the Illumina short reads of C. ×hytivus (S14) against each type of repeat, we estimated the proportion of repeats to be 62.68%, whereas the assembled repeat proportion is 39.54% of the estimated genome size (699.87 Mb) (Table S3, Supporting Information), suggesting that the remaining unassembled genome (≈23%) was mostly repeat sequences that were abnormally deeply covered by Illumina reads (Figure S3, Supporting Information)
We report the high-quality genome of a synthetic allotetraploid obtained using interspecific hybridization between cucumber (C. sativus) and its wild relative species (C. hystrix) and subsequent chromosome duplication, which is the first fully sequenced synthetic allopolyploid
Summary
Polyploids are organisms that contain three or more sets of chromosomes. They are mainly grouped into two types, autopolyploid and allopolyploid, depending on whether the multiple chromosome sets are identical or divergent. The prevalence of polyploids in nature demonstrates the evolutionary importance of polyploidy.[1] The success of allopolyploids suggests their evolutionary advantage owing to their increased diversity and plasticity.[2] allopolyploids face the challenge of coordinating distinct subgenomes with independent genetics and epigenetics into a single nucleus.[3] The merger of two or more divergent genomes is believed to cause “genomic shock” in the newly formed allopolyploid, resulting in genome-wide changes of gene structure and expression.[4] One of the subgenomes may become dominant over other subgenome(s) experiencing less sequence loss and higher homeologous gene expression.[5] In other instances, allopolyploids do not show subgenome
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