Hidden genetic variation shapes the structure of functional elements in Drosophila

Chakraborty, Mahul; VanKuren, Nicholas W.; Zhao, Roy; Zhang, Xinwen; Kalsow, Shannon; Emerson, J. J.

doi:10.1038/s41588-017-0010-y

Cited by 139 publications

(178 citation statements)

References 60 publications

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“…SVs including deletions and insertions could affect gene expression and phenotypic traits . In A. monticola , a total of 7 753 594 single nucleotide polymorphisms (SNPs), 17 226 deletions, and 7504 insertions were identified relative to A. duranensis and A. ipaensis genomes (Table S13a, Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Yin

Song

et al. 2019

Advanced Science

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Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.

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Section: Resultsmentioning

confidence: 99%

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Yin

Song

et al. 2019

Advanced Science

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“…Accumulating evidence suggests that most transposons in fly genome are still, although at a low frequency, capable of mobilizing, contributing to 79% of large genetic variation (Chakraborty et al, 2018; Kaminker et al, 2002). Examples include: Doc recently transposed into the white locus generated the first documented white-eye fly (Driver et al, 1989; Morgan, 1910); Accord mobilization contributes to the tandem duplication of the genes associated with nicotine resistance (Chakraborty et al, 2018); mdg3 inserted into the 3’UTR of mRpL48 and fritz (Chakraborty et al, 2018); copia mobilized into tonally (Chakraborty et al, 2018). Although these families are all targeted by the piRNA machinery (Senti et al, 2015), we barely detect any mobilization for them in all samples we examined, even upon blocking the piRNA pathway.…”

Section: Discussionmentioning

confidence: 99%

Hijacking Oogenesis Enables Massive Propagation of LINE and Retroviral Transposons

Wang

Dou

Moon

et al. 2018

Cell

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Although animals have evolved multiple mechanisms to suppress transposons, "leaky" mobilizations that cause mutations and diseases still occur. This suggests that transposons employ specific tactics to accomplish robust propagation. By directly tracking mobilization, we show that, during a short and specific time window of oogenesis, retrotransposons achieve massive amplification via a cell-type-specific targeting strategy. Retrotransposons rarely mobilize in undifferentiated germline stem cells. However, as oogenesis proceeds, they utilize supporting nurse cells-which are highly polyploid and eventually undergo apoptosis-as factories to massively manufacture invading products. Moreover, retrotransposons rarely integrate into nurse cells themselves but, instead, via microtubule-mediated transport, they preferentially target the DNA of the interconnected oocytes. Blocking microtubule-dependent intercellular transport from nurse cells significantly alleviates damage to the oocyte genome. Our data reveal that parasitic genomic elements can efficiently hijack a host developmental process to propagate robustly, thereby driving evolutionary change and causing disease.

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“…; but see Chakraborty et al. ), which may lead to fewer opportunities for local adaptation by way of major segregating inversions.…”

Section: Discussionmentioning

confidence: 99%

“…Genomic differentiation between tropical and temperate populations of Australian D. melanogaster has been linked to these inversion polymorphisms (Turner et al 2008;Kolaczkowski et al 2011;Fabian et al 2012;Kapun et al 2016). Inversion polymorphisms in D. melanogaster appear to be less common on the X-chromosomes compared to the autosomes (Charlesworth et al 1987;Kolaczkowski et al 2011;; but see Chakraborty et al 2018), which may lead to fewer opportunities for local adaptation by way of major segregating inversions.…”

Section: Predictions and Empirical Patternsmentioning

confidence: 99%

Quantifying the relative contributions of the X chromosome, autosomes, and mitochondrial genome to local adaptation*

et al. 2018

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During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X‐linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multigeneration crossing scheme, using two cline‐end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly—a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow.

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Hidden genetic variation shapes the structure of functional elements in Drosophila

Cited by 139 publications

References 60 publications

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Hijacking Oogenesis Enables Massive Propagation of LINE and Retroviral Transposons

Quantifying the relative contributions of the X chromosome, autosomes, and mitochondrial genome to local adaptation*

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