Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation

Griswold, Cortland K.; Asif, Saira

doi:10.1038/s41437-023-00595-9

Cited by 4 publications

(1 citation statement)

References 36 publications

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“…However, because the typical tract length of hGCs or double crossovers involving homoeologous chromosomes is not known, it is not possible to distinguish these two processes, which remains a topic for future work, presumably in a system that has more easily identifiable regions that have experienced hGC, HE, and double crossovers. Analytical methods to identify the frequency of occurrence and the allelic segregation patterns of double crossovers is an active area of research in autopolyploids (57, 58), but extending these methods to allopolyploids that experience HEs or hGC has received little attention.…”

Section: Discussionmentioning

confidence: 99%

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

Conover,

Grover,

Sharbrough

et al. 2023

Preprint

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A 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). This latter process 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 account for autapomorphic SNPs that may lead to similar patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. Here, 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. Using this new method, we find little evidence for homoeologous gene conversion in allopolyploid cottons and that only two of the forty best-supported events are shared by more than one species. We do, 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. Overall, our analyses demonstrate 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 highlight the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.SIGNIFICANCE STATEMENTAllopolyploidy is a prominent process in plant diversification, involving the union of two divergent genomes in a single nucleus via interspecific hybridization and genome doubling. The merger of genomes sets in motion a variety of inter-genomic and epigenomic interactions that are thought to lead to the origin of new phenotypes. Among these is recombinational exchange between duplicated chromosomes, which can involve sequence lengths ranging from several bases to entire chromosome arms, and which can be either reciprocal or unidirectional in their effects. Here we present a new analytical framework for detecting these inter-genomic recombinational processes in allopolyploids, and demonstrate that they have been rare in a group of allopolyploid species in the cotton genus.

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Section: Discussionmentioning

confidence: 99%

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

Conover,

Grover,

Sharbrough

et al. 2023

Preprint

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Defining autopolyploidy: Cytology, genetics, and taxonomy

Lv,

Addo Nyarko,

Ramtekey

et al. 2024

American J of Botany

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Autopolyploidy is taxonomically defined as the presence of more than two copies of each genome within an organism or species, where the genomes present must all originate within the same species. Alternatively, “genetic” or “cytological” autopolyploidy is defined by polysomic inheritance: random pairing and segregation of the four (or more) homologous chromosomes present, with no preferential pairing partners. In this review, we provide an overview of methods used to categorize species as taxonomic and cytological autopolyploids, including both modern and obsolete cytological methods, marker‐segregation‐based and genomics methods. Subsequently, we also investigated how frequently polysomic inheritance has been reliably documented in autopolyploids. Pure or predominantly polysomic inheritance was documented in 39 of 43 putative autopolyploid species where inheritance data was available (91%) and in seven of eight synthetic autopolyploids, with several cases of more mixed inheritance within species. We found no clear cases of autopolyploids with disomic inheritance, which was likely a function of our search methodology. Interestingly, we found seven species with purely polysomic inheritance and another five species with partial or predominant polysomic inheritance that appear to be taxonomic allopolyploids. Our results suggest that observations of polysomic inheritance can lead to relabeling of taxonomically allopolyploid species as autopolyploid and highlight the need for further cytogenetic and genomic investigation into polyploid origins and inheritance types.

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Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids

Conover,

Grover,

Sharbrough

et al. 2024

American J of Botany

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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 allopolyploid Gossypium species (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 in Gossypium, 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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Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation

Cited by 4 publications

References 36 publications

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids

Defining autopolyploidy: Cytology, genetics, and taxonomy

Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids

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