Insertion polymorphisms of mobile genetic elements in sexual and asexual populations of
            <i>Daphnia pulex</i>

Jiang, Xiaoqian; Tang, Haixu; Ye, Zhiqiang; Lynch, Michael

doi:10.1093/gbe/evw302

Cited by 10 publications

(16 citation statements)

References 66 publications

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“…Under the condition that the presence and/or absence of TE insertion have to be supported by at least five reads in ≥50 clones, a total of 17,658 polymorphic TE insertion sites were identified in the KAP population, including 2,263 (∼13%) reference TE insertion sites and 15,395 (∼87%) non-reference TE insertion sites. Compared with the previous comprehensive comparison of TE insertion difference between D. pulex asexual and sexual groups, we identified fewer TE insertions (17,658 in this study vs. 19,301 in eight sexual D. pulex clones, Jiang et al. 2017 ).…”

Section: Resultscontrasting

confidence: 73%

“…An early season sample with 96 clones was collected; sequencing reads were obtained on these clones and then were used to identify TE insertions in each clone (see Materials and Methods). The D. pulex TE library as input of our TE detection algorithms have been established in a previous study, which is a comprehensive D. pulex TE library annotated from two available D. pulex reference genome assemblies ( TCO and PA42 ), including 1,461 full length and 27,849 fragmented TE sequences ( Jiang et al. 2017 ).…”

Section: Resultsmentioning

confidence: 99%

“…2004 ), using scaffold_1 of D. pulex assembly PA42 (∼1.6 MB). Next, we randomly inserted a set of 100 TEs chosen from D. pulex TE library with the length about 2 KB ( Jiang et al. 2017 ).…”

Section: Methodsmentioning

confidence: 99%

“…The input of TE identification algorithms include: a D. pulex PA42 assembly as the reference genome ( Ye et al. 2017 ); a previously established D. pulex TE library consisting of 1,461 full-length and 27,849 fragmented TEs ( Jiang et al. 2017 ); and the whole-genome sequencing data from each of the 73 D. pulex clones from the KAP population.…”

Section: Methodsmentioning

confidence: 99%

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A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

Jiang

Tang

Ismail

et al. 2018

Molecular Biology and Evolution

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Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5normalX). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90normal%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70normal%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.

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Section: Resultscontrasting

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

Jiang

Tang

Ismail

et al. 2018

Molecular Biology and Evolution

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“…Comparison of the 2 assemblies did not reveal any contigs/ scaffolds unique to either MP or NMP clones. We also searched for transposable-element (TE) insertions using a preconstructed Daphnia TE library (24), but found no TEs unique to either group. These results suggest that NMP clones do not have unique shared, large genomic insertions/deletions or symbionts with causal contributions to the NMP trait.…”

Section: Resultsmentioning

confidence: 99%

Genetic control of male production in Daphnia pulex

Molinier

Zhao

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined by environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing ability is controlled by a dominant allele at a single locus. We identified the locus by comparing whole-genome sequences of 67 nonmale-producing (NMP) and 100 male-producing (MP) clones from 5 Daphnia pulex populations, revealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on chromosome I. These markers include 7 nonsynonymous mutations, all of which are located within one unannotated protein-coding gene (gene 8960). Within this single gene, all of the marker-linked NMP haplotypes from different populations form a monophyletic clade, suggesting a single origin of the NMP phenotype, with the NMP haplotype originating by introgression from a sister species, Daphnia pulicaria. Methyl farnesoate (MF) is the innate juvenile hormone in daphnids, which induces the production of males and whose inhibition results in female-only production. Gene 8960 is sensitive to treatment by MF in MP clones, but such responsiveness is greatly reduced in NMP clones. Thus, we hypothesize that gene 8960 is located downstream of the MF-signaling pathway in D. pulex, with the NMP phenotype being caused by expression change of gene 8960.

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Genome Evolution of Asexual Organisms and the Paradox of Sex in Eukaryotes

Hörandl

Bast

Brandt

et al. 2020

Evolutionary Biology—A Transdisciplinary Approach

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The predominance of sex in eukaryotes is still enigmatic. Sex, a composed process of meiosis and mixis cycles, confers high costs but the selective advantages remain unclear. In this review, we focus on potentially detrimental effects of asexuality on genome evolution. Theory predicts that asexual lineages should suffer from lack of meiotic DNA repair, accumulation of deleterious mutations, proliferation

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Insertion polymorphisms of mobile genetic elements in sexual and asexual populations of Daphnia pulex

Cited by 10 publications

References 66 publications

A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

Genetic control of male production in Daphnia pulex

Genome Evolution of Asexual Organisms and the Paradox of Sex in Eukaryotes

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