Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster

Guirao-Rico, Sara; González, Josefa

doi:10.1016/j.cois.2018.11.002

Cited by 9 publications

(6 citation statements)

References 67 publications

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“…melanogaster has adapted in recent evolutionary time to a wide-range of environmental conditions [26, 27]. Indeed, there are hundreds of genome sequences available from worldwide populations [28, 29]. This species has one of the best functionally annotated genomes, which facilitates the identification of traits under selection [30].…”

Section: Introductionmentioning

confidence: 99%

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

et al. 2019

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Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster , in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

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Section: Introductionmentioning

confidence: 99%

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

et al. 2019

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“…The biological and genetic tractability of fruit flies ( Drosophila and related genera) has led to their status as a premier model system for biological research, particularly in the genomic era (Clark et al, 2007;Hales et al, 2015) . Current publicly available genome assemblies number in the tens of species, some with accompanying gene expression and regulation databases (Chen et al, 2014;modENCODE Consortium et al, 2010) , comparative genomics tools (Stark et al, 2007) , or population genomic data (Guirao-Rico & González, 2019;Lack et al, 2016;Signor et al, 2018) . Unfortunately, these genomic resources are far from comprehensive for this remarkably biodiverse group, which encompasses over 1,600 described species (O'Grady & DeSalle, 2018) .…”

Section: Introductionmentioning

confidence: 99%

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang

Miller

et al. 2020

Preprint

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Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long read sequencing allow high quality genome assemblies for tens or even hundreds of species to be generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution within this key group.

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“…The large SSR and SNP data sets in our study can be used in Vespa velutina hornet control; these data can be used for DNA phenotyping identification [42], introgression estimation [43], and dispersal analyses of invasive pest [44]. They also can be used extend the study of Vespa velutina to evolution [45], molecular ecology [46], polymorphism, and genetic diversity [47].…”

Section: Discussionmentioning

confidence: 98%

De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Wang

Zheng

et al. 2020

Insects

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The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.

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Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster

Cited by 9 publications

References 67 publications

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Highly contiguous assemblies of 101 drosophilid genomes

De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

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