Highly contiguous assemblies of 101 drosophilid genomes

Kim, Bernard; Wang, Jeremy; Miller, Danny E.; Barmina, Olga; Delaney, Emily; Thompson, Ammon; Comeault, Aaron A.; Peede, David; D'Agostino, Emmanuel R. R.; Peláez, Julianne; Aguilar, Jessica M; Haji, Diler; Matsunaga, Teruyuki; Armstrong, Ellie E.; Zych, Molly; Ogawa, Yoshitaka; Stamenković‐Radak, Marina; Jelić, Mihailo; Veselinović, Marija Savić; Tanasković, Marija; Erić, Pavle; Gao, Jian‐Jun; Katoh, Takehiro K.; Toda, Masanori J.; Watabe, Hideaki; Watada, Masayoshi; Davis, Jeremy S; Moyle, Leonie C.; Manoli, Giulia; Bertolini, Enrico; Košťál, Vladimı́r; Hawley, R. Scott; Takahashi, Aya; Jones, Corbin D.; Price, Daniel O.; Whiteman, Noah K.; Kopp, Artyom; Matute, Daniel R.; Petrov, Dmitri A.

doi:10.1101/2020.12.14.422775

Cited by 18 publications

(30 citation statements)

References 65 publications

(82 reference statements)

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“…Second, we confirm that Zaprionus is related to the cardini/qunaria/immigrans group, consistent with O'Grady and DeSalle (2018) and Throckmorton (1975), but discordant with Russo et al (2013). Despite our well resolved phylogeny, comparisons with other studies emphasize the need to expand species sampling, especially given the potential to generate highly contiguous genomes at relatively low cost (Kim et al, 2020).…”

Section: Discussionsupporting

confidence: 84%

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Widespread introgression across a phylogeny of 155Drosophilagenomes

Suvorov

Kim

Wang

et al. 2020

Preprint

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Genome-scale sequence data has invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred, with introgression at the base of species radiations being particularly common. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

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Section: Discussionsupporting

confidence: 84%

“…Genome sequences used by this work were obtained from concurrent projects and public databases. Genome sequencing and assembly for 84 genomes is described in (Kim et al, 2020). These data are available for download at NCBI BioProject PRJNA675888.…”

Section: Genome Assemblies and Public Datamentioning

confidence: 99%

Widespread introgression across a phylogeny of 155Drosophilagenomes

Suvorov

Kim

Wang

et al. 2020

Preprint

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“…A time-calibrated species tree was inferred using the loci: 16S, COI, COII,ND2,28S,Gpdh1,Gstd1,Marf,l(2)tid (also known as Alg3 or Nltdi) and AdhR from 13 spp of Drosophila and four Scaptomyza spp. Scaptomyza sequences were accessed from the genomes in (Kim et al, 2020) and (Gloss et al, 2019) using tblastn searches for protein coding genes and blastn searches for the ribosomal RNA genes. The Adh Related gene appears to be deleted in S. flava and was coded as missing data.…”

Section: Time Calibrated Molecular Phylogeny Of Scaptomyza and Drosophila Sppmentioning

confidence: 99%

“…S. flava DNA sequences were previously published (Goldman-Huertas et al, 2015). Two more Scaptomyza sequences were obtained from (Kim et al, 2020) and (Gloss et al, 2019) including the non-leaf-mining species S. hsui and S. graminum (a leaf-miner on Caryophyllaceae spp). DNA sequences were aligned, partitioned by codon position, models fitted to all three partitions and chosen according to AICc (GTR+I+G) in IQ-Tree (Nguyen et al, 2015).…”

Section: Molecular Phylogeny Of Drosophilid Or67b Genesmentioning

confidence: 99%

Evolution of olfactory receptors tuned to mustard oils in herbivorous Drosophilidae

Matsunaga

Reisenman

Goldman-Huertas

et al. 2019

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248): 21 Plant toxins are effective defenses because they are aversive to most insects. The same 22 molecules, however, are co-opted as host-finding cues by specialist herbivores. Although such 23 behavioral shifts are central to our understanding of herbivorous insect diversification, it is not 24 well understood how these behaviors evolve. We addressed this in Scaptomyza flava, a 25 herbivorous drosophilid fly within a lineage that shifted to feeding on toxic mustard plants 26 (Brassicales) less than 10 million years ago. S flava lost the ancestral attraction to yeast volatiles 27 and the attendant chemoreceptors used to detect these odors. Here we report that S. flava, but not 28 its close microbe-feeding relatives Drosophila melanogaster and S. pallida, is attracted to 29 mustard host-plant odors, including volatile mustard oils (isothiocyanates or ITCs). Our genomic 30 analysis uncovered three S. flava paralogs of an olfactory receptor gene (Or67b) that likely 31 experienced recent positive selection. We then tested whether these chemoreceptors could 32 underlie the observed attraction to volatile ITCs. Our in vivo recordings revealed that two of the 33 S. flava Or67b proteins (Or67b1 and Or67b3) -but not the homologous Ors from microbe-34 feeding relatives -responded selectively and sensitively to volatile ITCs. These Ors are the first 35 ITC chemoreceptors other than TRP channel family (e.g., the TrpA1 'wasabi' receptor) known 36 from any animal. Remarkably, S. flava Or67b3 was sufficient to drive olfactory attraction toward 37 butyl ITC when expressed in an attractive olfactory circuit. Our study illuminates that ancestrally 38 aversive chemicals can be co-opted as attractants through gene duplication, leading to the origin 39 of hedonic valence shifts in herbivorous insects. 40 41 42Significance Statement (120) 43 Plant toxins trigger aversive olfactory (volatile-mediated) and gustatory (contact-mediated) 44 responses in animals. Paradoxically, toxic plants are often colonized by specialist insects that co-45 opt these toxins as host-plant finding cues. The mechanisms underlying these behavioral shifts, 46 from indifference or repulsion to plant chemicals, to attraction, remain unclear. To address this, 47 we used a fly lineage, Scaptomyza, that switched from yeast-feeding to feeding on mustard plants 48 less than 10 million years ago. We found that S. flava is attracted to mustard-plant odors and 49 volatile mustard oils (isothiocyanates or ITCs) such as 'wasabi', a behavior enabled by the 50 evolution of genes encoding odorant receptors highly sensitive to ITCs. Our study illuminates 51 how insects colonize toxic host plants through duplication and ecological repurposing of genes 52 encoding pre-existing chemoreceptors. 53 54 55 56 57 Many plant compounds used in food, agriculture and medicine originally evolved as 58 toxins that deter and repel enemies (1). Among the most well-known compounds are those 59 reactive electrophiles that induce the sensation of pain, such as diallyl disulfide a...

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“…We combine twelve new transcriptomes sequenced in this study with recently published genomes for two Hawaiian Drosophila species , four non-Hawaiian Scaptomyza 40 , and six outgroup species 41 . By increasing the number of genes used to infer relationships, we begin to unpack the evolutionary history in the short internodes at the base of the Hawaiian Drosophila radiation.…”

Section: Introductionmentioning

confidence: 99%

Phylotranscriptomics reveals discordance in the phylogeny of Hawaiian Drosophila and Scaptomyza (Diptera: Drosophilidae)

Church

Extavour

2021

Preprint

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Island radiations present natural laboratories for studying the evolutionary process. The Hawaiian Drosophil-idae are one such radiation, with nearly 600 described species and substantial morphological and ecological diversification. These species are largely divided into a few major clades, but the relationship between these clades remains uncertain. Here we present 12 new assembled transcriptomes from across these clades, and use these transcriptomes to resolve the base of the evolutionary radiation. We recover a new hypothesis for the relationship between clades, and demonstrate its support over previously published hypotheses. We then use the evolutionary radiation to explore dynamics of concordance in phylogenetic support, by analyzing the gene and site concordance factors for every possible topological combination of major groups. We show that high bootstrap values mask low evolutionary concordance, and we demonstrate that the most likely topology is distinct from the topology with the highest support across gene trees and from the topology with highest support across sites. We then combine all previously published genetic data for the group to estimate a time-calibrated tree for over 300 species of drosophilids. Finally, we digitize dozens of published Hawaiian Drosophilidae descriptions, and use this to pinpoint probable evolutionary shifts in reproductive ecology as well as body, wing, and egg size. We show that by examining the entire landscape of tree and trait space, we can gain a more complete understanding of how evolutionary dynamics play out across an island radiation.

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Highly contiguous assemblies of 101 drosophilid genomes

Cited by 18 publications

References 65 publications

Widespread introgression across a phylogeny of 155Drosophilagenomes

Widespread introgression across a phylogeny of 155Drosophilagenomes

Evolution of olfactory receptors tuned to mustard oils in herbivorous Drosophilidae

Phylotranscriptomics reveals discordance in the phylogeny of Hawaiian Drosophila and Scaptomyza (Diptera: Drosophilidae)

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