Highly contiguous assemblies of 101 drosophilid genomes

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

Hirtodrosophila nigrispina Chen & Katoh & Gao 2019, sp. nov.

<i>Hirtodrosophila nigrispina</i> Chen, Katoh & Gao, sp. nov. <p>(Figs 3 I–L, 5M–R, 10)</p> <p> <b>Diagnosis.</b> Epandrial ventral lobe with apical acute projection (Fig. 10D). Cercus ventrally with numerous black, thick spines nearly the same in size (Fig. 10E). Aedeagus apically broadened, medial margin flat in ventral view, with a pair of lateral processes and medial membranous protrusion (Fig. 10 J–L); lateral processes distally parallel with each other in ventral view, finely serrate on dorsal margin (Fig. 10J, N).</p> <p> <b>Description</b> (characters commonly seen in <i>H. zhangae</i> <b>sp. nov.</b> not repeated) (♂, ♀). Head (Figs 3I, J, 5 M–R): Frontal vitta brown. Fronto-orbital plate dark brown, anteriorly paler. Ocellar setae inserted slightly inside triangle made by ocelli. Face and facial carina brown, ventrally darker. Gena yellowish brown, anteriorly darker. First flagellomere dark grayish brown. Supracervical setae ca. 10 per side; postocular setae 23–26 per side. Clypeus brown to dark brown. Palpus pale grayish yellow, with one apical and 1–2 subapical, prominent setae. Cibarium with ca. seven medial and 23–25 posterior sensilla per side.</p> <p>Legs (Fig. 3I): Foreleg 1st tarsomere shorter than total length of four succeeding tarsomeres. Mid- and hindleg 1st tarsomeres slightly shorter than or as long as total length of four succeeding tarsomeres.</p> <p>Abdomen (Fig. 3I, L): Caudal bands medially often narrowed or interrupted.</p> <p>Male terminalia (Fig. 10 A–N): Epandrium with ca. 28 long setae per side. Cercus with 37–41 long setae, ventral ones thicker. Surstylus ventrally tapered and vent posteriad, with upper row of ca. six prensisetae, and lower row of ca. seven prensisetae; inner surface with ca. 18 long setae, anterior ones longer and thinner; anterior margin with ca. four short setulae. Tenth sternite anteromedially concaved, somewhat heart-shaped in ventral view. Paramere with ca. five minute sensilla along apical to dorsosubapical margin. Aedeagal apodeme straight, thin, much shorter than and fused to aedeagus.</p> <p>Female terminalia (Fig. 10 O–Q): Tergite VIII grayish brown to dark grayish brown, pubescent dorsally to caudolaterally. Oviscapt valve distally somewhat quadrate in lateral view, with ca. four lateral and ca. 16 marginal, peg-like ovisensilla. Spermathecal capsule slightly broader than long, with introvert about 4/5 height of capsule; introvert only scarcely wrinkled.</p> <p>Measurements (in mm): BL = 2.88 in holotype (range in 4♀ paratypes: 2.94–3.45), ThL = 1.22 (1.24–1.29), WL = 3.34 (3.24–3.46), WW = 1.40 (1.38–1.52).</p> <p>Indices: FW/HW = 0.52 (range in 4♀ paratypes: 0.49–0.50), ch/o = 0.26 (0.17–0.20), prorb = 0.74 (0.66–0.84), rcorb = 0.32 (0.27–0.44), vb = 0.40 (0.33–0.40), orbito = 0.64 (0.55–0.65), dcl = 0.60 (0.53–0.58), sctl = 1.18 (1.08–1.20), sterno = 0.40 (0.55–0.84), dcp = 0.47 (0.39–0.48), sctlp = 1.44 (1.12–1.16), C = 3.44 (3.15–3.38), 4c = 0.66 (0.66–0.73), 4v = 1.47 (1.43–1.55), 5x = 1.52 (1.61–1.83), ac = 2.48 (2.42–2.87), M = 0.43 (0.45–0.49), C3F = 0.37 (0.34–0.42).</p> <p> <i>Holotype</i>. ♂ (#06472), CHINA: Danyunxia Station, Huanglong Nature Reserve, Ngawa, Sichuan, 32°43'36" N, 104°02'55" E, 2,140 m, 16.ix.2018, <i>ex</i> banana trap, J.J. Gao, W.F. Zhang, and Y.F. Zou.</p> <p> <i>Paratypes</i>. CHINA: 4♀ (#06473, #06475−77), same data as holotype.</p> <p> <b>Distribution.</b> China (Sichuan).</p> <p> <b>Etymology.</b> Referring to the black, thick spines on ventral portion of cercus.</p> <p> <b>Remarks.</b> The paratype female specimens were identified as conspecific with the holotype male specimen #06472 by morphological similarity, though the body color pattern of #06472 rather indistinct than females. Considering the insufficiency of evidence of species-level divergence between the holotype and paratype specimens, we tentatively describe them as of the same species.</p>Published as part of <i>Chen, Yu, Katoh, Takehiro K. & Gao, Jian-Jun, 2019, The Hirtodrosophila melanderi species group (Diptera: Drosophilidae) from the Huanglong National Nature Reserve, Sichuan, China, pp. 113-131 in Zootaxa 4623 (1)</i> on pages 127-130, DOI: 10.11646/zootaxa.4623.1.7, <a href="http://zenodo.org/record/3253618">http://zenodo.org/record/3253618</a&gt

Hirtodrosophila zouae Chen & Katoh & Gao 2019, sp. nov.

<i>Hirtodrosophila zouae</i> Chen, Katoh & Gao, sp. nov. <p>(Figs 3 E–H, 5G–L, 9)</p> <p> <b>Diagnosis.</b> Cercus ventrally with numerous black, thick spines including ca. four long, inner marginal ones (Fig. 9D). Aedeagus apically with large membranous process which tapering distally in lateral view, subapically swollen dorsally, with a pair of lateral processes, with a pair of lateral processes and a series of small acute projections ventrally (Fig. 9 I–M); lateral processes small, flat, finely serrate on dorsal margin (Fig. 9I, L, M).</p> <p> <b>Description</b> (characters commonly seen in <i>H. zhangae</i> <b>sp. nov.</b> not repeated) (♂). Head (Figs 3E, F, 5 G–L): Gena yellowish brown to brown, anteriorly dark brown. First flagellomere grayish yellow; arista with five dorsal branches. Supracervical setae 13–16 per side; postocular setae 26–29 per side. Cibarium with ca. seven medial and ca. 18 posterior sensilla per side.</p> <p>Thorax (Fig. 3E, F): Postpronotal lobe yellowish brown. Mesonotum yellowish brown to brown; stripes sometimes very indistinct.</p> <p>Male terminalia (Fig. 9): Epandrium with ca. 38 long setae per side. Cercus with ca. 36 long setae. Surstylus ventrally tapered with upper row of ca. eight prensisetae, and lower row of 7−8 prensisetae; inner surface with ca. 24 long setae; anterior margin with ca. seven short setulae. Paramere apically with ca. five minute sensilla. Aedeagal apodeme slightly curved, about 1/2 length of aedeagus.</p> <p>Measurements (in mm): BL = 3.06 in holotype (range in 2♂ paratypes: 2.56–3.00), ThL = 1.24 (1.14–1.22), WL = 3.24 (2.94–3.24), WW = 1.40 (1.28–1.38).</p> <p>Indices: FW/HW = 0.52 (range in 2♂ paratypes: 0.49–0.52), ch/o = 0.22 (0.15–0.19), prorb = 0.74 (0.79–0.83), rcorb = 0.32 (0.32–0.39), vb = 0.41 (0.38–0.43), orbito = 0.75 (0.54–0.64), dcl = 0.64 (0.52–0.56), sctl = 1.08 (1.06–1.08), sterno = 0.72 (0.64–0.66), dcp = 0.42 (0.46–0.49), sctlp = 1.35 (1.11–1.18), C = 3.42 (3.33), 4c = 0.67 (0.67–0.69), 4v = 1.44 (1.44–1.47), 5x = 1.28 (1.30–1.36), ac = 2.08 (2.45–2.50), M = 0.41 (0.38–0.42), C3F = 0.35 (0.33–0.37).</p> <p> <i>Holotype</i>. ♂ (#06468), CHINA: Danyunxia Station, Huanglong Nature Reserve, Ngawa, Sichuan, 32°43'36" N, 104°02'55" E, 2,140 m, 16.ix.2018, <i>ex</i> banana trap, J.J. Gao, W.F. Zhang, and Y.F. Zou.</p> <p> <i>Paratypes</i>. CHINA: 2♂ (#06469, #06471), same data as holotype.</p> <p> <b>Distribution.</b> China (Sichuan).</p> <p> <b>Etymology.</b> Patronym, in honor of Ms. Yu-Fang Zou (IBCAS) for help in field collection.</p>Published as part of <i>Chen, Yu, Katoh, Takehiro K. & Gao, Jian-Jun, 2019, The Hirtodrosophila melanderi species group (Diptera: Drosophilidae) from the Huanglong National Nature Reserve, Sichuan, China, pp. 113-131 in Zootaxa 4623 (1)</i> on page 127, DOI: 10.11646/zootaxa.4623.1.7, <a href="http://zenodo.org/record/3253618">http://zenodo.org/record/3253618</a&gt

The Hirtodrosophila melanderi species group (Diptera: Drosophilidae) from the Huanglong National Nature Reserve, Sichuan, China

Chen, Yu, Katoh, Takehiro K., Gao, Jian-Jun (2019): The Hirtodrosophila melanderi species group (Diptera: Drosophilidae) from the Huanglong National Nature Reserve, Sichuan, China. Zootaxa 4623 (1): 113-131, DOI: https://doi.org/10.11646/zootaxa.4623.1.

Data from: Maternally transmitted non-bacterial male killer in Drosophila biauraria

A maternally inherited, all-female trait is widely found among arthropods, which is caused by bacterial endosymbionts such as Wolbachia, Rickettsia, Spiroplasma and Cardinium We discovered a single female of Drosophila biauraria, collected from Tomakomai, Hokkaido, Japan, that produced all-female offspring. This all-female trait was maternally inherited in the iso-female line (SP12F) by backcrossing with males of a normal line (SP11-20) with a 1:1 sex ratio derived from the same population. The all-female trait was not affected by tetracycline treatment performed for two consecutive generations. However, the microinjection of filter-sterilised homogenate of SP12F females into SP11-20 females established all-female matrilines. Our data suggest the role of transmissible agents, most likely viruses, but not bacteria or protists, as the possible cause of the all-female phenotype, which is likely to be achieved by killing of male embryos because egg hatch rates of SP12F were nearly half as those of SP11-20. This is the first report in Diptera to demonstrate a maternally inherited virus-like element as the cause of the male-killing phenotype in D. biauraria

Lordiphosa spatulata Katoh & Zhang & Toda & Zhang & Gao 2018, sp. nov.

<i>Lordiphosa spatulata</i> Katoh & Gao, sp. nov. <p>(Pls 2E, 3M, 4M, 6E, 7M; Fig. 15)</p> <p> <b>Diagnosis.</b> Cercus ventrally elongated, with a tuft of 6–7 spines around ventral apex (Fig. 15C,D,F). Hypandrial caudolateral lobes unpubescent (Fig. 15I –K). Paramere nearly straight but slightly sinuate subapically, apically pointed (Fig. 15I –L). Gonopods dorsomedially roundly concaved in lateral view, sharply angled at caudoventral corners (Fig. 15K,L). Aedeagus apically somewhat dilated in ventral view (Fig. 15I); apodeme directed at acute angle to aedeagus (Fig. 15K).</p> <p> <b>Description</b> (characters commonly seen in <i>L</i>. <i>yangi</i> <b>sp. nov.</b> not repeated) (♂). Head (Pls 2E, 3M, 4M, 6E, 7M): Frontal vitta, fronto-orbital plate, and ocellar triangle yellowish brown. Occiput medially paler. Postgena dark brown, laterally somewhat paler. Antennal 1 st flagellomere pale yellow; arista with 4 dorsal and 2 ventral branches. Supracervical setulae 13¯15 per side; postocular setae 16–19 per side. Clypeus brown, dorsally darker. Cibarium with ca. 24 medial and ca. 17 posterior sensilla per side. Prementum with 5 (1 proximal, 2 lateral, and 2 distal) pairs of setae.</p> <p>Thorax (Pl. 2E) yellowish brown. Mesonotum caudomedially darker, without stripe. Acrostichal setulae in ca. 6 irregular rows. Mid katepisternal seta distinctly longer than those below it.</p> <p>Legs (Pl. 2E, Fig. 15A,B): Male foreleg with 2, 2, and 1 transverse sex-combs on 1st, 2nd, and 3rd tarsomeres, respectively; each row consisting of 2–4 teeth. Fore- and midleg 1 st tarsomeres nearly as long as total length of 4 succeeding tarsomeres.</p> <p>Abdomen (Pl. 2E): Tergites grayish brown, caudally with dark grayish brown, narrow, marginal bands.</p> <p>Male terminalia (Fig. 15C–L): Epandrium dorsomedially pale yellowish brown, with ca. 16 long setae per side; ventral lobe apically narrowly extended. Cercus pubescent except for lateral margin, with ca. 21 long setae; lateral margin sclerotized. Surstylus with a row of 1 3–15 prensisetae on caudodorsal margin and ca. 22 recurved setae on ventral portion of inner surface. Aedeagus membranous except for apical portion, subapically to medially sheathed with gonopods; apodeme rod-shaped, not dilated apically, much shorter than aedeagus.</p> <p>Measurements (in mm): BL = 2.27 in holotype, ThL = 1.12, WL = 2.87, WW = 1.16.</p> <p>Indices: FW/HW = 0.53, ch/o = 0.16, prorb = 0.85, rcorb = 0.29, vb = 0.40, orbito = 0.43, dcl = 0.54, sctl = 1.33, sterno = 0.47, dcp = 0.50, sctlp = 1.05, C = 4.05, 4c = 0.60, 4v = 1.61, 5x = 1.84, ac = 2.00, M = 0.52, C3F = 0.40.</p> <p> <b> PLATE 3. Head (anterior view) and postocciput (caudal view) of <i>Lordiphosa</i> species.</b> A, <i>L. denticeps</i> (Okada & Sasakawa, 1956) (#06025); B, <i>L. neokurokawai</i> (Singh & Gupta, 1981) (#06010); C, <i>L. ramula</i> Zhang, 1993 (#06008); D, <i>L. tripartita</i> (Okada, 1966) (#06049); E, <i>L. mikioides</i> <b>sp. nov.</b> (paratype #06061); F, <i>L. kimurai</i> <b>sp. nov.</b> (paratype #06066); G, <i>L. anthophilia</i> <b>sp. nov.</b> (paratype #05606); H, <i>L. yangi</i> <b>sp. nov.</b> (paratype #06035); I, <i>L. tibetica</i> <b>sp. nov.</b> (paratype #06030); J, <i>L. medogensis</i> <b>sp. nov.</b> (paratype #06007); K, <i>L. hamatispina</i> <b>sp. nov.</b> (holotype #06027); L, <i>L. secula</i> <b>sp. nov.</b> (paratype #06045); M, <i>L. spatulata</i> <b>sp. nov.</b> (holotype #06034). Abbreviations: poc s = postocellar setae, spc s = supracervical setulae.</p> <p> <b> PLATE 4. Antenna of <i>Lordiphosa</i> species.</b> A, <i>L. denticeps</i> (Okada & Sasakawa, 1956) (#06025); B, <i>L. neokurokawai</i> (Singh & Gupta, 1981) (#06010); C, <i>L. ramula</i> Zhang, 1993 (#06008); D, <i>L. tripartita</i> (Okada, 1966) (#06049); E, <i>L. mikioides</i> <b>sp. nov.</b> (paratype ♀); F, <i>L. kimurai</i> <b>sp. nov.</b> (paratype ♀); G, <i>L. anthophilia</i> <b>sp. nov.</b> (paratype #05609); H, <i>L. yangi</i> <b>sp. nov.</b> (paratype #06035); I, <i>L. tibetica</i> <b>sp. nov.</b> (paratype #06030); J, <i>L. medogensis</i> <b>sp. nov.</b> (paratype #06007); K, <i>L. hamatispina</i> <b>sp. nov.</b> (holotype #06027); L, <i>L. secula</i> <b>sp. nov.</b> (paratype #06045); M, <i>L. spatulata</i> <b>sp. nov.</b> (holotype #06034).</p> <p> <b>Holotype.</b> ♂ (#06034), Mt. Duoxiongla, Linzhi, Xizang, China, 3,500–3,800 m a.s.l., 24.ix.2010, J.J. Gao (KIZ).</p> <p> <b>Distribution.</b> China (Xizang).</p> <p> <b>Etymology.</b> From Latin word “ spatulata ” (meaning “like spatula”), referring to the apical shape of paramere somewhat likes painting-knife.</p> <p> <b>Remarks.</b> This species resembles <i>L. tripartita</i>, <i>L. paradenticeps</i>, <i>L. vittata</i>, <i>L. gruicollara,</i> and <i>L. eminens</i> in sharing the following characters: cercus ventrally elongated (except for <i>L. paradenticeps</i>), with a tuft of spines around ventral apex; paramere basally not so strongly curved; aedeagal apodeme rod-shaped, apically not dilated, much shorter than aedeagus; hypandrial caudolateral lobes unpubescent. However, this species can easily be distinguished from them by the paramere nearly straight but slightly sinuate subapically and the gonopods sharply angled at caudoventral corners.</p> <p> <b> PLATE 5. Cibarium (dorsal and lateral view) of <i>Lordiphosa</i> species (1).</b> A, <i>L. denticeps</i> (Okada & Sasakawa, 1956) (#06025); B, <i>L. neokurokawai</i> (Singh & Gupta, 1981) (#06010); C, <i>L. ramula</i> Zhang, 1993 (#06008); D, <i>L. tripartita</i> (Okada, 1966) (#06049); E, <i>L. mikioides</i> <b>sp. nov.</b> (holotype #06060); F, <i>L. kimurai</i> <b>sp. nov.</b> (paratype #06066); G, <i>L. anthophilia</i> <b>sp. nov.</b> (paratype #05606); H, <i>L. yangi</i> <b>sp. nov.</b> (paratype #06035);. Abbreviations: cly = clypeus, m s = medial sensilla, p s = posterior sensilla, s c = sensilla campaniformia.</p> <p> <b> PLATE 6. Cibarium of <i>Lordiphosa</i> species (2).</b> A, <i>L. tibetica</i> <b>sp. nov.</b> (paratype #06030); B, <i>L. medogensis</i> <b>sp. nov.</b> (paratype #06007); C, <i>L. hamatispina</i> <b>sp. nov.</b> (holotype #06027); D, <i>L. secula</i> <b>sp. nov.</b> (paratype #06045); E, <i>L. spatulata</i> <b>sp. nov.</b> (holotype #06034).</p>Published as part of <i>Katoh, Takehiro K., Zhang, Guang, Toda, Masanori J., Zhang, Wen-Xia & Gao, Jian-Jun, 2018, The Lordiphosa denticeps species group (Diptera: Drosophilidae) in China, with redescriptions of four known species and descriptions of nine new species, pp. 37-75 in Zootaxa 4471 (1)</i> on pages 66-71, DOI: 10.11646/zootaxa.4471.1.2, <a href="http://zenodo.org/record/1439521">http://zenodo.org/record/1439521</a&gt