DrosoPhyla: genomic resources for drosophilid phylogeny and systematics

Finet, Cédric; Va, Kassner; Ab, Carvalho; Chung, Henry; Day, John; Ek, Delaney; Fc, De Re; Hd, Dufour; Dupim, Eduardo G; Hf, Izumitani; Tb, Gauterio; Justen, Jessa; Katoh, Takahiko; Kopp, Artyom; Koshikawa, Shigeyuki; Longdon, Ben; El, Loreto; Nunes,; Kk, Raja; Rebeiz, Mark; Ritchie, MG; Saakyan, G. A.; Sneddon, Tanya; Teramoto, Machiko; Tyukmaeva, Venera; Vanderlinde, Thyago; Ee, Wey; Werner, Thomas; Williams, Tom A.; Lj, Robe; Toda, Masanori J.; Marlétaz, Ferdinand

doi:10.1101/2021.03.23.436709

Cited by 5 publications

(1 citation statement)

References 93 publications

(113 reference statements)

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“…One species of each of the genera Leucophenga and Chymomyza , both contained in less-studied sister subfamily Steganinae, have also been sequenced. We note some taxonomic inconsistencies arising from the paraphyly or polyphyly of certain drosophilid taxa ( Finet et al, 2021 ; O'Grady and DeSalle, 2018 ; Yassin, 2013 ) but will make no attempt to address those issues here. The sequenced species originate from mainland and island locations in North America, Europe, Africa, and Asia; are distributed from northern (e.g.…”

Section: Resultsmentioning

confidence: 99%

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang²,

Miller

et al. 2021

eLife

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158

198

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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 efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory 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 at the scale of hundreds of species.

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Section: Resultsmentioning

confidence: 99%

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang²,

Miller

et al. 2021

eLife

Self Cite

158

198

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Phylogeny and evolution of mycophagy in the Zygothrica genus group (Diptera: Drosophilidae)

Zhang

Katoh

Finet

et al. 2021

Molecular Phylogenetics and Evolution

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Efficient k-mer based curation of raw sequence data: application inDrosophila suzukii

Gautier

2023

Preprint

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Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient kmer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 32 Pool-Seq samples of the invasive species Drosophila suzukii. We first used CLARK software to build a dictionary of species-discriminating kmers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k-mers composing each query sample sequence that matched a discriminating k-mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were assigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of >60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.

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DrosoPhyla: genomic resources for drosophilid phylogeny and systematics

Cited by 5 publications

References 93 publications

Highly contiguous assemblies of 101 drosophilid genomes

Highly contiguous assemblies of 101 drosophilid genomes

Phylogeny and evolution of mycophagy in the Zygothrica genus group (Diptera: Drosophilidae)

Efficient k-mer based curation of raw sequence data: application inDrosophila suzukii

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