Dataset Information

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly.

ABSTRACT: The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.

SUBMITTER: Warren WC

PROVIDER: S-EPMC5866774 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly.

Warren Wesley C WC García-Pérez Raquel R Xu Sen S Lampert Kathrin P KP Chalopin Domitille D Stöck Matthias M Loewe Laurence L Lu Yuan Y Kuderna Lukas L Minx Patrick P Montague Michael J MJ Tomlinson Chad C Hillier LaDeana W LW Murphy Daniel N DN Wang John J Wang Zhongwei Z Garcia Constantino Macias CM Thomas Gregg C W GCW Volff Jean-Nicolas JN Farias Fabiana F Aken Bronwen B Walter Ronald B RB Pruitt Kim D KD Marques-Bonet Tomas T Hahn Matthew W MW Kneitz Susanne S Lynch Michael M Schartl Manfred M

Nature ecology & evolution 20180212 4

The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heteroz ...[more]

PMID: 29434351

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Project description:BackgroundMoso bamboo (Phyllostachys edulis) is a typical East Asian bamboo that does not flower for > 60 years and propagates without seed reproduction. Thus, Moso bamboo can be propagated vegetatively, possibly resulting in highly heterozygous genetic inheritance. Recently, a draft genome of Moso bamboo was reported, followed by whole genome single nucleotide polymorphisms (SNP) analysis, which showed that the genome of Moso bamboo in China has regional characteristics. Moso bamboo in Japan is thought to have been introduced from China over the sea in 1736. However, it is unclear where and how Moso bamboo was introduced in Japan from China. Here, based on detailed analysis of heterozygosity in genome diversity, we estimate the spread of genome diversity and its pedigree of Moso bamboo.ResultsWe sequenced the whole genome of Moso bamboo in Japan and compared them with data reported previously from 15 regions of China. Only 4.1 million loci (0.37% of the analyzed genomic region) were identified as polymorphic loci. We next narrowed down the number of polymorphic loci using several filters and extracted more reliable SNPs. Among the 414,952 high-quality SNPs, 319,431 (77%) loci were identified as heterozygous common to all tested samples. The result suggested that all tested samples were clones via vegetative reproduction. Somatic mutations may accumulate in a heterozygous manner within a single clone. We examined common heterozygous loci between samples from Japan and elsewhere, from which we inferred that an individual closely related to the sample from Fujian, China, was introduced to Japan across the sea without seed reproduction. In addition, we collected 16 samples from four nearby bamboo forests in Japan and performed SNP and insertion/deletion analyses using a genotyping by sequencing (GBS) method. The results suggested that a small number of somatic mutations would spread within and between bamboo groves.ConclusionsHigh heterozygosity in the genome-wide diversity of Moso bamboo implies the vegetative propagation of Moso bamboo from China to Japan, the pedigree of Moso bamboo in Japan, and becomes a useful marker to approach the spread of genome diversity in clonal plants.

Dataset Information

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly.

Publications

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly.

Similar Datasets

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