Dataset Information

Unzipping haplotypes in diploid and polyploid genomes.

ABSTRACT: Diploid genomes consist of two homologous copies of chromosomes with one from each parent while polyploid genomes contain more than two homologous sets of chromosomes. Most of the reference genome assemblies collapsed haplotypes that represent 'mosaic' sequences, ignoring allelic variants that may be involved in important cellular and biological functions. Unzipping haplotypes into distinct sets of sequences has been a growing trend in recent genome studies, as it is an essential tool towards resolving important clinical and biological questions, such as compound heterozygotes, heterosis, and evolution. Herein, we review existing methods for alignment-based and assembly-based haplotype phasing for heterozygous diploid and polyploid genomes, as well as recent advances of experimental approaches for improved genome phasing. We anticipate that full haplotype phasing could become a routine procedure in genome studies in the near future.

SUBMITTER: Zhang X

PROVIDER: S-EPMC6938933 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Unzipping haplotypes in diploid and polyploid genomes.

Zhang Xingtan X Wu Ruoxi R Wang Yibin Y Yu Jiaxin J Tang Haibao H

Computational and structural biotechnology journal 20191209

Diploid genomes consist of two homologous copies of chromosomes with one from each parent while polyploid genomes contain more than two homologous sets of chromosomes. Most of the reference genome assemblies collapsed haplotypes that represent 'mosaic' sequences, ignoring allelic variants that may be involved in important cellular and biological functions. Unzipping haplotypes into distinct sets of sequences has been a growing trend in recent genome studies, as it is an essential tool towards re ...[more]

PMID: 31908732

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Project description:BackgroundSpecies complexes or aggregates consist of a set of closely related species often of different ploidy levels, whose relationships are difficult to reconstruct. The N Hemisphere Achillea millefolium aggregate exhibits complex morphological and genetic variation and a broad ecological amplitude. To understand its evolutionary history, we study sequence variation at two nuclear genes and three plastid loci across the natural distribution of this species complex and compare the patterns of such variations to the species tree inferred earlier from AFLP data.ResultsAmong the diploid species of A. millefolium agg., gene trees of the two nuclear loci, ncpGS and SBP, and the combined plastid fragments are incongruent with each other and with the AFLP tree likely due to incomplete lineage sorting or secondary introgression. In spite of the large distributional range, no isolation by distance is found. Furthermore, there is evidence for intragenic recombination in the ncpGS gene. An analysis using a probabilistic model for population demographic history indicates large ancestral effective population sizes and short intervals between speciation events. Such a scenario explains the incongruence of the gene trees and species tree we observe. The relationships are particularly complex in the polyploid members of A. millefolium agg.ConclusionsThe present study indicates that the diploid members of A. millefolium agg. share a large part of their molecular genetic variation. The findings of little lineage sorting and lack of isolation by distance is likely due to short intervals between speciation events and close proximity of ancestral populations. While previous AFLP data provide species trees congruent with earlier morphological classification and phylogeographic considerations, the present sequence data are not suited to recover the relationships of diploid species in A. millefolium agg. For the polyploid taxa many hybrid links and introgression from the diploids are suggested.

Project description:BACKGROUND AND AIMS:Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medica, C. micrantha and C. reticulata. METHODS:A genotyping by sequencing library was established with the restriction enzyme ApeKI applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. KEY RESULTS:Among 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time. CONCLUSIONS:The pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. It will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomic fragments. It can also be used for the first generations of interspecific breeding schemes.

Dataset Information

Unzipping haplotypes in diploid and polyploid genomes.

Publications

Unzipping haplotypes in diploid and polyploid genomes.

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