Homoeologs: What Are They and How Do We Infer Them?

Glover, Natasha; Redestig, Henning; Dessimoz, Christophe

doi:10.1016/j.tplants.2016.02.005

Cited by 160 publications

(136 citation statements)

References 102 publications

Supporting

Mentioning

130

Contrasting

Unclassified

Order By: Relevance

“…Analyzing these NWG genomic data revealed thousands of genome-wide SNP markers for its genetic diversity analysis. Thus, it is technically possible to sample genome-wide genetic variability in plants with complex genomes through GBS, even though SNP calling from sequences of a complex, polyploid genome is confounded by the presence of homeologs [54], orthologs, and paralogs [55]. Thousands of SNP markers would be more informative for plant genetic diversity analysis with higher resolution than the several hundreds of AFLP markers normally screened in previous studies [50,51,56,57].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Bhattarai

Peterson

et al. 2018

Diversity

View full text Add to dashboard Cite

Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for the molecular characterization of plant germplasm with complex and unsequenced genomes. This study represents the first preliminary effort using GBS to discover genome-wide genetic variants of northern wheatgrass (Elymus lanceolatus ssp. lanceolatus (Scribn. and J. G. Sm.) Gould) plants and to assess the genetic diversity present in four cultivated and six wild accessions. The effort generated the first novel set of genomic resources and 5659 single nucleotide polymorphism (SNP) markers for this tetraploid grass. The diversity analysis revealed 8.8% of SNP variation residing among the 10 accessions and 1.9% SNP variation present between cultivated and wild accessions. The Bayesian analysis identified three major clusters of the assayed samples, and the principal coordinates analysis revealed the genetic distinctness of the two accessions collected from Nevada and Wyoming. The flow cytometry analysis confirmed the tetraploid nature of some of the assayed samples and estimated the average genome size to be 9.3-9.4 Gb for this species. These findings are useful for the genetic improvement of this native grass species for forage production and rangeland reclamation. The findings are also encouraging for the broad application of genotyping-by-sequencing in the characterization of genome-wide genetic variability in non-model polyploid plants.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Bhattarai

Peterson

et al. 2018

Diversity

View full text Add to dashboard Cite

show abstract

“…‘Homoeologous exchanges’ specifically describe exchanges of large chromosomal segments that result from crossover formation between homoeologous chromosomes (i.e. inherited from divergent parental species and re‐united within a single allopolyploid genome; Glover et al ., ) via the meiotic homologous recombination pathway (Sharpe et al ., ; Gaeta & Pires, and references therein). This type of event is thus unique to allopolyploids and frequent in the first generations following allo‐polyploidisation (e.g.…”

Section: Introductionmentioning

confidence: 99%

Homoeologous exchanges cause extensive dosage‐dependent gene expression changes in an allopolyploid crop

et al. 2017

View full text Add to dashboard Cite

SummaryStructural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined.Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop.We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time.This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.

show abstract

“…1B;Manton, 1950;Wagner & Chen, 1965;Hickok & Klekowski, 1974;Wagner, 1974;Hickok, 1977;Reichenstein, 1981). Rare, completely fertile homoploid hybrids, such as Pteris quadriaurita Â multiaurita reported by Walker (1958Walker ( , 1962, result from crosses between sexual species with low genetic divergence and exhibit full pairing of homoeologs (i.e., chromosome copies derived from different progenitor species; Glover et al, 2016) at meiosis. Additional studies have reported homoploid hybrids with spore germination rates as high as 29-40% and gametophytes producing functional sperm and/or eggs (Walker, 1958(Walker, , 1962Whittier & Wagner, 1971;Bierhorst, 1977;Conant, 1990;Mayer & Mesler, 1993;Mullenniex et al, 1998).…”

Section: Homoploid Hybridsmentioning

confidence: 99%

Genetic and genomic aspects of hybridization in ferns

Sigel

2016

J of Sytematics Evolution

View full text Add to dashboard Cite

The morphological and ecological intermediacy of hybrid taxa has long interested and challenged fern biologists, resulting in numerous systematic contributions focused on disentangling relationships within reticulate species complexes. From a genetic perspective, hybrid ferns are especially interesting because they represent the union of divergent parental genomes in unique evolutionary entities. This review summarizes advances in our knowledge of the genetic and genomic aspects of hybridization in ferns from the mid-20th century to the present. The different organismal products of hybridization, evolutionary aspects of additive and non-additive gene expression in allopolyploids, genetic and genomic mechanisms leading to gene silencing and loss, the roles of multiple origins and introgression for imparting genetic variation to hybrid fern taxa and their progenitors, and the utility of allopolyploid ferns to investigate mechanisms of genome evolution in the homosporous ferns are discussed. Comparisons are made to other plant lineages and important future research directions are highlighted, with the goal of stimulating additional research on hybrid ferns.

show abstract

Homoeologs: What Are They and How Do We Infer Them?

Cited by 160 publications

References 102 publications

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Homoeologous exchanges cause extensive dosage‐dependent gene expression changes in an allopolyploid crop

Genetic and genomic aspects of hybridization in ferns

Contact Info

Product

Resources

About