Progressive Cactus alignment of 298 drosophilid species

NIAID Data Ecosystem2026-05-01 收录

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Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. Whole-genome sequence alignments link evolution at the nucleotide level across species and are a critical but computationally intensive step for downstream genomic analyses. Progressive Cactus is a reference-free, whole-genome alignment tool designed to scale to alignments of thousands of species. In the study associated with this dataset, we conducted Oxford Nanopore long-read sequencing of both inbred lines and single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections. We selected a set of 298 suitably high-quality drosophilid genomes from this study, from publicly available genomes assembled previously by us, and genomes assembled by other studies. Repeats were identified and soft-masked in each genome with RepeatModeler2 and RepeatMasker. A guide tree was constructed from 1,000 single-copy orthologs annotated by BUSCO v5 in all genomes. Individual gene trees were inferred with IQTREE2 and a species tree was estimated from the gene trees with ASTRAL-MP. The tree was scaled by the substitution rate at 4-fold degenerate sites and provided to Progressive Cactus as the guide tree for the alignment. Detailed methods are provided in the study. The alignment is released as an open resource and as a tool for studying evolution at the scale of an entire insect family. Methods The following table lists the set of genomes incorporated into the alignment. Note that accessions will be updated once genomes are processed through NCBI GenBank. name genome source genome accession Stegana nigrithorax NCBI GenBank PENDING Leucophenga maculata NCBI GenBank PENDING Leucophenga montana NCBI GenBank PENDING Cacoxenus indagator NCBI GenBank PENDING Amiota minor NCBI GenBank PENDING Amiota communis NCBI GenBank PENDING Amiota mariae NCBI GenBank PENDING Chymomyza caudatula NCBI GenBank PENDING Chymomyza procnemis NCBI GenBank PENDING Chymomyza amoena NCBI GenBank PENDING Chymomyza costata NCBI GenBank GCA_018150985.1 Chymomyza fuscimana NCBI GenBank GCA_949987675.1 Scaptodrosophila lebanonensis NCBI RefSeq GCF_003285725.1 Scaptodrosophila latifasciaeformis NCBI GenBank PENDING Hirtodrosophila duncani NCBI GenBank PENDING Lordiphosa mommai NCBI GenBank GCA_018904225.1 Lordiphosa collinella NCBI GenBank PENDING Lordiphosa andalusiaca NCBI GenBank PENDING Lordiphosa fenestrarum NCBI GenBank PENDING Lordiphosa magnipectinata NCBI GenBank PENDING Lordiphosa clarofinis NCBI GenBank GCA_018904275.1 Drosophila sturtevanti NCBI GenBank GCA_018150375.1 Drosophila emarginata NCBI GenBank PENDING Drosophila neocordata NCBI GenBank GCA_018903615.1 Drosophila saltans NCBI GenBank GCA_018903575.1 Drosophila austrosaltans NCBI GenBank PENDING Drosophila prosaltans NCBI GenBank GCA_018151275.1 Drosophila sucinea NCBI GenBank GCA_018150745.1 Drosophila nebulosa NCBI GenBank GCA_024703675.1 Drosophila insularis NCBI GenBank GCA_018903935.1 Drosophila tropicalis NCBI GenBank GCA_018151085.1 Drosophila willistoni NCBI RefSeq GCF_018902025.1 Drosophila paulistorum NCBI GenBank GCA_018152135.1 Drosophila equinoxialis NCBI GenBank GCA_018150345.1 Drosophila guanche NCBI RefSeq GCF_900245975.1 Drosophila subobscura NCBI RefSeq GCF_008121235.1 Drosophila bifasciata NCBI GenBank GCA_009664405.1 Drosophila subsilvestris NCBI GenBank PENDING Drosophila obscura NCBI RefSeq GCF_018151105.1 Drosophila ambigua NCBI GenBank GCA_018150905.1 Drosophila tristis NCBI GenBank GCA_018150885.1 Drosophila lowei NCBI GenBank GCA_008121275.1 Drosophila miranda NCBI RefSeq NCBI GenBank Drosophila pseudoobscura NCBI RefSeq GCF_009870125.1 Drosophila persimilis NCBI RefSeq GCF_003286085.1 Drosophila helvetica NCBI RefSeq PENDING Drosophila azteca NCBI GenBank GCA_005876895.1 Drosophila affinis NCBI GenBank PENDING Drosophila algonquin NCBI GenBank PENDING Drosophila athabasca NCBI GenBank GCA_008121215.1 Drosophila setifemur NCBI GenBank GCA_021224005.1 Drosophila ironensis NCBI GenBank GCA_021223825.1 Drosophila varians NCBI GenBank GCA_018150405.1 Drosophila vallismaia NCBI GenBank PENDING Drosophila merina NCBI GenBank PENDING Drosophila ercepeae NCBI GenBank GCA_018150545.1 Drosophila pseudoananassae NCBI GenBank GCA_018153035.1 Drosophila malerkotliana NCBI GenBank GCA_018153235.1 Drosophila bipectinata NCBI RefSeq GCF_018153845.1 Drosophila parabipectinata NCBI GenBank GCA_018153455.1 Drosophila atripex NCBI GenBank PENDING Drosophila monieri NCBI GenBank PENDING Drosophila pandora NCBI GenBank GCA_021223865.1 Drosophila anomalata NCBI GenBank PENDING Drosophila ananassae NCBI RefSeq GCF_017639315.1 Drosophila pallidosa NCBI GenBank PENDING Drosophila oshimai NCBI GenBank GCA_018150695.1 Drosophila ficusphila NCBI RefSeq GCF_018152265.1 Drosophila gunungcola NCBI RefSeq GCF_025200985.1 Drosophila elegans NCBI RefSeq GCF_018152505.1 Drosophila fuyamai NCBI GenBank GCA_018153365.1 Drosophila kurseongensis NCBI GenBank GCA_018153305.1 Drosophila rhopaloa NCBI RefSeq GCF_018152115.1 Drosophila carrolli NCBI GenBank GCA_018152295.1 Drosophila biarmipes NCBI RefSeq GCF_025231255.1 Drosophila subpulchrella NCBI RefSeq GCF_014743375.2 Drosophila suzukii NCBI RefSeq GCF_013340165.1 Drosophila mimetica NCBI GenBank PENDING Drosophila takahashii NCBI RefSeq GCF_018152695.1 Drosophila lutescens NCBI GenBank PENDING Drosophila pseudotakahashii NCBI GenBank PENDING Drosophila prostipennis NCBI GenBank PENDING Drosophila eugracilis NCBI RefSeq GCF_018153835.1 Drosophila melanogaster NCBI RefSeq GCF_000001215.4 Drosophila simulans NCBI RefSeq GCF_016746395.2 Drosophila mauritiana NCBI RefSeq GCF_004382145.1 Drosophila sechellia NCBI RefSeq GCF_004382195.2 Drosophila orena NCBI GenBank GCA_005876975.1 Drosophila erecta NCBI RefSeq GCF_003286155.1 Drosophila teissieri NCBI RefSeq GCF_016746235.2 Drosophila santomea NCBI RefSeq GCF_016746245.2 Drosophila yakuba NCBI RefSeq GCF_016746365.2 Drosophila pectinifera NCBI GenBank GCA_008042775.1 Drosophila triauraria NCBI GenBank GCA_014170255.2 Drosophila auraria NCBI GenBank GCA_008042615.1 Drosophila tani NCBI GenBank GCA_008042535.1 Drosophila rufa NCBI GenBank GCA_018153105.1 Drosophila asahinai NCBI GenBank GCA_008042795.1 Drosophila lacteicornis NCBI GenBank GCA_008044355.1 Drosophila kanapiae NCBI GenBank GCA_008042475.1 Drosophila ogumai NCBI GenBank GCA_018904815.1 Drosophila kikkawai NCBI RefSeq GCF_018152535.1 Drosophila bocki NCBI GenBank GCA_008042715.1 Drosophila leontia NCBI GenBank GCA_008042735.1 Drosophila watanabei NCBI GenBank GCA_008042575.1 Drosophila punjabiensis NCBI GenBank GCA_008042585.1 Drosophila serrata NCBI GenBank PENDING Drosophila bunnanda NCBI GenBank PENDING Drosophila truncata NCBI GenBank GCA_008042515.1 Drosophila birchii NCBI GenBank PENDING Drosophila mayri NCBI GenBank GCA_008042485.1 Drosophila anomelani NCBI GenBank PENDING Drosophila jambulina NCBI GenBank GCA_018152175.1 Drosophila seguyi NCBI GenBank GCA_008042675.1 Drosophila vulcana NCBI GenBank GCA_008042555.1 Drosophila bakoue NCBI GenBank GCA_008044335.1 Drosophila tsacasi NCBI GenBank GCA_018904565.1 Drosophila nikananu NCBI GenBank GCA_008042635.1 Drosophila bocqueti NCBI GenBank GCA_018151655.1 Drosophila burlai NCBI GenBank GCA_008042655.1 Drosophila busckii NCBI RefSeq GCF_011750605.1 Drosophila repletoides NCBI GenBank GCA_018150835.1 Liodrosophila aerea NCBI GenBank PENDING Hypselothyrea guttata NCBI GenBank PENDING Zaprionus bogoriensis NCBI GenBank PENDING Zaprionus ghesquierei NCBI GenBank GCA_018904095.1 Zaprionus inermis NCBI GenBank GCA_018151445.1 Zaprionus kolodkinae NCBI GenBank GCA_018901885.1 Zaprionus tuberculatus Zaprionus tsacasi NCBI GenBank GCA_018904105.1 Zaprionus ornatus NCBI GenBank GCA_018904035.1 Zaprionus africanus NCBI GenBank GCA_018151435.1 Zaprionus gabonicus NCBI GenBank GCA_018903695.1 Zaprionus indianus NCBI GenBank GCA_018904595.1 Zaprionus capensis NCBI GenBank GCA_018903675.1 Zaprionus taronus NCBI GenBank GCA_018901805.1 Zaprionus davidi NCBI GenBank GCA_018903715.1 Zaprionus vittiger NCBI GenBank GCA_018904025.1 Zaprionus lachaisei NCBI GenBank GCA_018901815.1 Zaprionus nigranus NCBI GenBank GCA_018903425.1 Zaprionus camerounensis NCBI GenBank GCA_018904165.1 Drosophila quadrilineata NCBI GenBank GCA_018150725.1 Drosophila pruinosa NCBI GenBank GCA_018150935.1 Drosophila rubida NCBI GenBank PENDING Drosophila hypocausta NCBI GenBank PENDING Drosophila siamana NCBI GenBank PENDING Drosophila immigrans NCBI GenBank GCA_018153375.1 Drosophila formosana NCBI GenBank PENDING Drosophila ustulata NCBI GenBank PENDING Drosophila niveifrons NCBI GenBank PENDING Drosophila sulfurigasteralbostrigata NCBI GenBank GCA_023558435.1 Drosophila sulfurigasterbilimbata NCBI GenBank GCA_023558465.1 Drosophila sulfurigastersulfurigaster NCBI GenBank GCA_023558475.1 Drosophila kohkoa NCBI GenBank GCA_019972355.1 Drosophila pallidifrons NCBI GenBank GCA_023558445.1 Drosophila kepulauana NCBI GenBank GCA_023558455.1 Drosophila nasuta NCBI GenBank GCA_023558535.1 Drosophila albomicans NCBI RefSeq GCF_009650485.2 Drosophila tripunctata NCBI GenBank PENDING Drosophila cardini NCBI GenBank GCA_018903735.1 Drosophila parthenogenetica NCBI GenBank PENDING Drosophila acutilabella NCBI GenBank PENDING Drosophila dunni NCBI GenBank GCA_018152125.1 Drosophila nigrodunni NCBI GenBank GCA_020829145.1 Drosophila arawakana NCBI GenBank GCA_018151165.1 Drosophila macrospina NCBI GenBank PENDING Drosophila funebris NCBI GenBank GCA_958295475.1 Drosophila putrida NCBI GenBank PENDING Drosophila neotestacea NCBI GenBank PENDING Drosophila testacea NCBI GenBank PENDING Drosophila histrio NCBI GenBank GCA_958299025.1 Drosophila kuntzei NCBI GenBank PENDING Drosophila phalerata NCBI GenBank GCA_951394115.1 Drosophila innubila NCBI GenBank GCA_004354385.2 Drosophila falleni NCBI GenBank PENDING Drosophila rellima NCBI GenBank PENDING Drosophila quinaria NCBI GenBank PENDING Drosophila suboccidentalis NCBI GenBank PENDING Drosophila subquinaria NCBI GenBank PENDING Drosophila recens NCBI GenBank PENDING Zygothrica flavofinira NCBI GenBank PENDING Hirtodrosophila trivittata NCBI GenBank PENDING Hirtodrosophila cameraria NCBI GenBank GCA_949708635.1 Hirtodrosophila histrioides NCBI GenBank PENDING Hirtodrosophila confusa NCBI GenBank PENDING Hirtodrosophila alboralis NCBI GenBank PENDING Drosophila lacertosa NCBI GenBank GCA_004143845.1 Drosophila colorata NCBI GenBank PENDING Drosophila robusta NCBI GenBank PENDING Drosophila sordidula NCBI GenBank PENDING Drosophila micromelanica NCBI GenBank GCA_004143825.1 Drosophila nigromelanica NCBI GenBank GCA_004149465.1 Drosophila melanica NCBI GenBank GCA_004143765.1 Drosophila paramelanica NCBI GenBank PENDING Drosophila lacicola NCBI GenBank PENDING Drosophila montana NCBI GenBank PENDING Drosophila borealis NCBI GenBank PENDING Drosophila littoralis NCBI GenBank GCA_018903485.1 Drosophila kanekoi NCBI GenBank PENDING Drosophila ezoana NCBI GenBank PENDING Drosophila virilis NCBI RefSeq GCF_003285735.1 Drosophila novamexicana NCBI RefSeq GCF_003285875.2 Drosophila americana NCBI GenBank GCA_030788265.1 Drosophila pseudotalamancana NCBI GenBank PENDING Drosophila nannoptera NCBI GenBank GCA_020883555.1 Drosophila pachea NCBI GenBank GCA_020883565.1 Drosophila gaucha NCBI GenBank PENDING Drosophila pegasa NCBI GenBank PENDING Drosophila mettleri NCBI GenBank PENDING Drosophila hydei NCBI RefSeq GCF_003285905.1 Drosophila eohydei NCBI GenBank PENDING Drosophila anceps NCBI GenBank PENDING Drosophila leonis NCBI GenBank PENDING Drosophila nigricruria NCBI GenBank PENDING Drosophila fulvimacula NCBI GenBank PENDING Drosophila peninsularis NCBI GenBank PENDING Drosophila repleta NCBI GenBank PENDING Drosophila paranaensis NCBI GenBank PENDING Drosophila mercatorum NCBI GenBank GCA_961210405.1 Drosophila meridionalis NCBI GenBank PENDING Drosophila meridiana NCBI GenBank PENDING Drosophila stalkeri NCBI GenBank PENDING Drosophila buzzatii NCBI GenBank PENDING Drosophila koepferae NCBI GenBank GCA_023375715.1 Drosophila antonietae NCBI GenBank GCA_030914385.1 Drosophila borborema NCBI GenBank GCA_030914335.1 Drosophila hamatofila NCBI GenBank PENDING Drosophila mayaguana NCBI GenBank PENDING Drosophila aldrichi NCBI GenBank PENDING Drosophila mulleri NCBI GenBank PENDING Drosophila mojavensis NCBI RefSeq GCF_018153725.1 Drosophila arizonae NCBI RefSeq GCF_001654025.1 Drosophila flavopinicola NCBI GenBank PENDING Drosophila maculinotata NCBI GenBank PENDING Scaptomyza hsui NCBI GenBank GCA_018152825.1 Scaptomyza graminum NCBI GenBank GCA_018901835.1 Scaptomyza polygonia NCBI GenBank PENDING Scaptomyza flava NCBI GenBank GCA_030179655.1 Scaptomyza montana NCBI GenBank GCA_018904305.1 Scaptomyza caliginosa NCBI GenBank PENDING Scaptomyza parva NCBI GenBank PENDING Scaptomyza pallida NCBI GenBank GCA_018152965.1 Scaptomyza reducta NCBI GenBank PENDING Scaptomyza tumidula NCBI GenBank PENDING Scaptomyza cyrtandrae NCBI GenBank PENDING Drosophila setosimentum NCBI GenBank PENDING Drosophila picticornis NCBI GenBank PENDING Drosophila anomalipes NCBI GenBank PENDING Drosophila quasianomalipes NCBI GenBank PENDING Drosophila cyrtoloma NCBI GenBank PENDING Drosophila melanocephala NCBI GenBank PENDING Drosophila differens NCBI GenBank PENDING Drosophila planitibia NCBI GenBank PENDING Drosophila silvestris NCBI GenBank PENDING Drosophila heteroneura NCBI GenBank PENDING Drosophila basisetae NCBI GenBank PENDING Drosophila paucipuncta NCBI GenBank PENDING Drosophila glabriapex NCBI GenBank PENDING Drosophila macrothrix NCBI GenBank PENDING Drosophila hawaiiensis NCBI GenBank PENDING Drosophila crucigera NCBI GenBank PENDING Drosophila pullipes NCBI GenBank PENDING Drosophila grimshawi NCBI RefSeq GCF_018153295.1 Drosophila engyochracea NCBI GenBank PENDING Drosophila villosipedis NCBI GenBank PENDING Drosophila ochracea NCBI GenBank PENDING Drosophila sproati NCBI GenBank GCA_018904355.1 Drosophila murphyi NCBI GenBank GCA_018904325.1 Drosophila dives NCBI GenBank PENDING Drosophila multiciliata NCBI GenBank PENDING Drosophila demipolita NCBI GenBank PENDING Drosophila longiperda NCBI GenBank PENDING Drosophila fungiperda NCBI GenBank PENDING Drosophila melanosoma NCBI GenBank PENDING Drosophila mimica NCBI GenBank PENDING Drosophila kambysellisi NCBI GenBank PENDING Drosophila infuscata NCBI GenBank PENDING Drosophila cognata NCBI GenBank PENDING Drosophila yooni NCBI GenBank PENDING Drosophila tanythrix NCBI GenBank PENDING Drosophila kokeensis NCBI GenBank PENDING Drosophila nrfundita NCBI GenBank PENDING Drosophila cracens NCBI GenBank PENDING Drosophila paracracens NCBI GenBank PENDING Drosophila imparisetae NCBI GenBank PENDING Drosophila nigritarsus NCBI GenBank PENDING Drosophila nrmedialis2 NCBI GenBank PENDING Drosophila nrmedialis3 NCBI GenBank PENDING Drosophila seclusa NCBI GenBank PENDING Drosophila kupee NCBI GenBank PENDING Drosophila kuia NCBI GenBank PENDING Drosophila atroscutellata NCBI GenBank PENDING Drosophila trichaetosa NCBI GenBank PENDING Drosophila neutralis NCBI GenBank PENDING Drosophila percnosoma NCBI GenBank PENDING Drosophila incognita NCBI GenBank PENDING Drosophila conformis NCBI GenBank PENDING Drosophila sordidapex NCBI GenBank PENDING

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2023-12-01

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