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Abstract PremiseA complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non‐crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. MethodsHere, we use an expanded phylogenetic sampling of high‐quality genome assemblies from seven allopolyploidGossypiumspecies (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. ResultsWe found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best‐supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. ConclusionsOverall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon inGossypium, affecting between zero and 24 genes per subgenome (0.0–0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four‐taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.
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Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective
Summary Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo‐allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far‐reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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- PAR ID:
- 10409585
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 238
- Issue:
- 6
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- p. 2284-2304
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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