DOI: 10.5061/dryad.x0k6djhrd
title: Progressive Cactus alignment of 298 drosophilid species

description: 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.
description: 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
description: # Progressive Cactus alignment of 298 drosophilid species A Progressive
 Cactus whole-genome, reference-free alignment was built with 298
 drosophilid genomes as listed in our preprint The Cactus alignment was
 broken up with GNU split to facilitate upload and download. Please
 download all the parts and run: *cat drosophila.hal. &gt;
 drosophila.hal* The Progressive Cactus tools must to be installed to
 utilize the alignments. One representative genome is used for each
 species. The genome's name in the alignment is the first letter of
 the genus name, underscore, and full species name, all caps. For example,
 "*Drosophila melanogaster*" is *"D_MELANOGASTER".* A
 summary of the data in the alignment can be viewed with: *halStats
 drosophila.hal*