Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in <i>Drosophila</i>

Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.</p

Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila

Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system

A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes

Gene duplication is supposed to be the major source for genetic innovations. However, how a new duplicate gene acquires functions by integrating into a pathway and results in adaptively important phenotypes has remained largely unknown. Here, we investigated the biological roles and the underlying molecular mechanism of the young kep1 gene family in the Drosophila melanogaster species subgroup to understand the origin and evolution of new genes with new functions. Sequence and expression analysis demonstrates that one of the new duplicates, nsr (novel spermatogenesis regulator), exhibits positive selection signals and novel subcellular localization pattern. Targeted mutagenesis and whole-transcriptome sequencing analysis provide evidence that nsr is required for male reproduction associated with sperm individualization, coiling, and structural integrity of the sperm axoneme via regulation of several Y chromosome fertility genes post-transcriptionally. The absence of nsr-like expression pattern and the presence of the corresponding cis-regulatory elements of the parental gene kep1 in the pre-duplication species Drosophila yakuba indicate that kep1 might not be ancestrally required for male functions and that nsr possibly has experienced the neofunctionalization process, facilitated by changes of trans-regulatory repertories. These findings not only present a comprehensive picture about the evolution of a new duplicate gene but also show that recently originated duplicate genes can acquire multiple biological roles and establish novel functional pathways by regulating essential genes

Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes

<p>Abstract</p> <p>Background</p> <p>Kraits (genus <it>Bungarus</it>) and cobras (genus <it>Naja</it>) are two representative toxic genera of elapids in the old world. Although they are closely related genera and both of their venoms are very toxic, the compositions of their venoms are very different. To unveil their detailed venoms and their evolutionary patterns, we constructed venom gland cDNA libraries and genomic bacterial artificial chromosome (BAC) libraries for <it>Bungarus multicinctus </it>and <it>Naja atra</it>, respectively. We sequenced about 1500 cDNA clones for each of the venom cDNA libraries and screened BAC libraries of the two snakes by blot analysis using four kinds of toxin probes; <it>i.e</it>., three-finger toxin (3FTx), phospholipase A2 (PLA2), kunitz-type protease inhibitor (Kunitz), and natriuretic peptide (NP).</p> <p>Results</p> <p>In total, 1092 valid expressed sequences tags (ESTs) for <it>B. multicinctus </it>and 1166 ESTs for <it>N. atra </it>were generated. About 70% of these ESTs can be annotated as snake toxin transcripts. 3FTx (64.5%) and <it>β </it>bungarotoxin (25.1%) comprise the main toxin classes in <it>B. multicinctus</it>, while 3FTx (95.8%) is the dominant toxin in <it>N. atra</it>. We also observed several less abundant venom families in <it>B. multicinctus </it>and <it>N. atra</it>, such as PLA2, C-type lectins, and Kunitz. Peculiarly a cluster of NP precursors with tandem NPs was detected in <it>B. multicinctus</it>. A total of 71 positive toxin BAC clones in <it>B. multicinctus </it>and <it>N. atra </it>were identified using four kinds of toxin probes (3FTx, PLA2, Kunitz, and NP), among which 39 3FTx-postive BACs were sequenced to reveal gene structures of 3FTx toxin genes.</p> <p>Conclusions</p> <p>Based on the toxin ESTs and 3FTx gene sequences, the major components of <it>B. multicinctus </it>venom transcriptome are neurotoxins, including long chain alpha neurotoxins (<it>α</it>-ntx) and the recently originated <it>β </it>bungarotoxin, whereas the <it>N. atra </it>venom transcriptome mainly contains 3FTxs with cytotoxicity and neurotoxicity (short chain <it>α</it>-ntx). The data also revealed that tandem duplications contributed the most to the expansion of toxin multigene families. Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (<it>dN</it>/<it>dS</it>) indicates that not only multigene toxin families but also other less abundant toxins might have been under rapid diversifying evolution.</p

Lamprigera morator

Lamprigera morator (Olivier, 1891) Figs 76–81 Lamprophorus morator Olivier, 1891: 596 (Type locality: Burma). Lamprigera morator: McDermott 1966:76. Diagnosis. This species has short oblong body (BW/BL approximate 0.60). Its pronotum is semi-elliptical with two translucent windows and a median longitudinal ridge. Male genitalia medial lobe thin, a little longer than parameres. Redescription of our male specimens (Figs 76–78). Body short oblong. BL: 15.9–16.8 mm; BW: 9.7–10.1 mm; BW/BL approximate 0.60. Coloration (Figs 76–78): head black; pronotum with a black pentagonal pronotal disc and other area yellow-brown, having two translucent windows at anterior edge; scutellum dark brown; elytra dark brown with a little light brown pilosity; tibiae, tarsi, and ventrites I–V brown to dark brown. Head. Large with big compound eyes, PW/GHW = 2–1.83; compound eyes kidney-shaped in lateral view and almost contiguous ventrally. Antennae clavate, short, only slightly longer than the diameter of a compound eye, barely exceeding the front edge of pronotum in transverse condition, thickly hirsute, first antennomere cylindrical and as long as second, second narrower, 3–10segments triangular, last antennomere bifurcate apically. Mandibles curved, slender, and sharply pointed; maxillary palp 5-segmented, apical segment circular; labial palp bi-segmented and pointed. Thorax. Pronotum (Fig. 78) semi-elliptical (PW/PL = 1.51–1.57) with two translucent windows and a median longitudinal ridge. Scutellum triangular. Elytra oblong, thinly pilose. Legs slender. Abdomen. Abdominal terga with posterior angles acutely projected posteriad, increasingly arcuate posteriad. Pygidium with circular lateral margins and posterior edge centrally depressed. Ventrite VII semi-circular. Male genitalia (Figs 79–81 ). Aedeagus sheath 1.65 mm long, covering dorsal side of male genitalia, with broadly rounded base. Aedeagus 1.96 mm long, sclerotised. Basal piece oblong and smooth, shorter than parameres. Medial lobe thin, a little longer than parameres. Parameres symmetrical, hypertrophic, close to the medial lobe, subparallel sided, tapering from half their length. Females. Unknown. Immatures. According to pairwise nucleotide distances of COI, two larval populations from Fugong (Lg11-L) and Yongde (Lg15-L) (both with a distance of 0.035 to male population) are identified as the same species. Material examined. CHINA: Yunnan: two &male;, Mangbing Village, Mangbing Township, Zhenkang County, Lincang Prefecture, 20.VIII.2007, leg. Xin-Wang Yang (Lg14); Six larvae, Nujiang Prefecture, Fugong County, Yapingshikuliudi, 26.IV.2004, leg. Xue-Yan Li (Lg11-L); Four larvae, Wumulong Township, Lincang City, Yongde County, 10.XI.2006, leg. De-Cai Ouyang (Lg15-L). Distribution. Burma; China: Yunnan (Zhenkang, Yongde, Fugong). Remarks. By comparing these specimens with the type specimens (Figs 16–18, 43), the clade 6 (Table 3) can be identified as L. morato, originally recorded in Burma (Olivier 1891). This species is similar to L. magnapronotum sp. nov in shape of the pronotum and male genitalia, but can be separated based on the yellow brown femurs of L. morator.Published as part of Dong, Zhiwei, Yiu, Vor, Liu, Guichun, He, Jinwu, Zhao, Ruoping, Peng, Yanqiong & Li, Xueyan, 2021, Three new species of Lamprigera Motschulsky (Coleoptera, Lampyridae) from China, with notes on known species, pp. 441-468 in Zootaxa 4950 (3) on pages 458-460, DOI: 10.11646/zootaxa.4950.3.2, http://zenodo.org/record/464996

Lamprigera minor

Lamprigera minor (Olivier, 1885) Figs 70–75 Lamprophorus minor Olivier, 1885: 345 (Type locality: Burma). Lamprigera minor: McDermott, 1966: 76. Diagnosis. This species has oblong body (BW/BL approximate 0.42), pronotum with central disc black and other areas yellow-brown, two transparent windows at the anterior edge; legs with tibae and tarsi brown; Male genitalia medial lobe strong, longer than parameres. Redescription of our male specimens (Figs 70–72). Body oblong. BL: 15.2–16.1 mm; BW: 6.2–7.1 mm; BW/ BL approximate 0.42. Coloration (Figs 70–72): head black; pronotum with central disc black and other areas yellow-brown, two transparent windows at the anterior edge; elytra dark brown with light yellow fluff; scutellum dark brown; ventral side of thorax brown; legs with tibae and tarsi brown; ventral side with head, tibiae, tarsi, ventrites I–IV brown, and ventrites V–VII yellow-brown. Head. Large with big compound eyes, PW/GHW = 1.58–1.66; compound eyes kidney-shaped in lateral view and almost contiguous ventrally; interspace between eyes concave. Antennae clavate, short, slightly longer than the diameter of a compound eye, slightly exceeding the front edge of the pronotum in transverse view, thickly hirsute, first antennomere cylindrical and as long as second, second narrower, 3-10 segments triangular, last antennomere flat. Mandibles curved, slender and sharply pointed; maxillary palp 5-segmented, apical segment circular; labial bi-segmented and pointed. Thorax. Pronotum (Fig. 72) semi–elliptical (PW/PL = 1.53–1.63), with wide translucent edges and centrally round black disc. Scutellum small, triangular. Elytra oblong, basal disc strongly convex, with a lot of fluff. Male genitalia (Figs 73–75). Aedeagus sheath 1.15 mm long, covering dorsal side of male genitalia, with base broadly rounded. Aedeagus 1.38 mm long, heavily sclerotised. Basal piece oblong and smooth, shorter than parameres. Medial lobe strong, longer than parameres. Parameres symmetrical with their top weakly triangular. Females. According to pairwise nucleotide distances of COI, one female population from Tengchong (Yunnan) (Lg10-F) (with a distance of 0.019 to the Yunnan male population (Lg11)) is identified as the same species. Immatures. Unknown. Material examined. CHINA: Yunnan: nine &male;, Yapingliuli, Lumadeng Village, Fugong County, Nujiang Prefecture, 1622 m, 15.VIII.2005, leg. Qin-Bai Hou (Lg11); Two &female;, Baoshan City, Tengchong County, Qushi, 21.X.2003, leg. Xue-Yan Li (Lg10–F). Taiwan: Nine &male;, Shouka, Shizi Township, Pindong County, 430 m, 4.XII.2016, leg. Wen-I Chou (Lg27). Distribution. Burma; China: Taiwan (Pingdong), Yunnan (Fugong, Tengchong). Remarks. By comparing with the type specimens (Figs 4–6, 39), we identified clade 4 (Table 3) as L. minor, which was originally recorded in Burma (Olivier 1885). This species is very similar to L. alticola (Figs 52–57) and L. luquanensis (Figs 58–63) but can be separated by having no dark brown area at the flanks of the semi-elliptical central black disc of pronotum in latter two. One of the populations was collected from Fugong (Lg11) bordering Burma. Although one male population was collected from Taiwan (Lg27), far from Yunnan, it has only a very small distance of nucleotide sequence (0.019); therefore, they are identified as the same species as the Yunnan population; the morphology is comparable with similar body and elytra shapes.Published as part of Dong, Zhiwei, Yiu, Vor, Liu, Guichun, He, Jinwu, Zhao, Ruoping, Peng, Yanqiong & Li, Xueyan, 2021, Three new species of Lamprigera Motschulsky (Coleoptera, Lampyridae) from China, with notes on known species, pp. 441-468 in Zootaxa 4950 (3) on pages 457-458, DOI: 10.11646/zootaxa.4950.3.2, http://zenodo.org/record/464996

Lamprigera

Diagnosis of Lamprigera male adults Head totally concealed by pronotum dorsally (Fig. 94); eyes kidney-shaped in lateral view and almost contiguous ventrally (Fig. 95); vertex broadly impressed between eyes (Fig. 95); antennae short, usually no longer than pronotum, 11–segmented, antennomeres 1–2 long and dilated, antennomeres 4–10 or 7–10 serrate, last antennomere briefly bifurcate apically. Pronotum (Fig. 96) well-developed, semi-elliptical, with black central disc and varied translucent edge, as important diagnostic traits for species identification. Abdomen with seven visible sternites (visible sternite = ventrite); abdominal tergites strongly lobed. Luminous organs spot-like, each located in sublateral sides of last abdominal ventrite (i.e. ventrite VII). Male genitalia with medial lobe slender in dorsal/ventral aspect, moderately broad in lateral aspect; parameres subparallel sided, thick and evenly broad, as an important diagnostic character for species identification. Key to Chinese Lamprigera species (excl. L. angustior and L. scutatu s) 1 Pronotum (Figs. 54, 60, 72, 96) with translucent or light brown area around anterior edge and posterolateral sides of black central disc.......................................................................................... 2 - Pronotum (Figs. 66, 78, 84, 90) only with translucent area at its anterior half and with posterior area darkbrown.......... 6 2 Pronotum (Fig. 96) with triangular black central disc......................................................... 3 - Pronotum (Figs. 54, 60, 72) with semielliptical black central disc............................................... 4 3 Elytra (Fig. 94) all black.......................................................... L. yunnana (Fairmaire, 1897) - Elytra (Fig. 10) with a narrow yellowish brown rim around outer margin...................... L. taimoshana Yiu, 2017 4 Two expanded dark brown area at the two sides of semielliptical black central disc (Figs. 66, 78)...................... 5 - No dark brown area at the two sides of semielliptical black central disc (Fig. 72)................ L. minor (Olivier, 1885) 5 Medial lobe of male genitalia twice as much as parameres in length (Figs. 55, 56)............ L. alticola Dong & Li, sp. n. - Medial lobe only a little longer than parameres (Figs. 61, 62)......................... L. luquanensis Dong & Li, sp. n. 6 Parameres with blunt end, pronotum with a thin yellow brown area at posterior edge (Figs. 90-92)................................................................................................ L. nitidicollis (Fairmaire, 1891) - Parameres with more or less pointed end................................................................... 7 7 End of parameres sharply pointed (Figs. 67, 68)............................... L. magnapronotum Dong & Li, sp. n. - End of parameres only a little pointed..................................................................... 8 8 Body oblong, BW/BL approximate 0.47.............................................. L. nepalensis (Hope, 1831) - Body wide, BW/BL approximate 0.6................................................. L. morator (Olivier, 1891)Published as part of Dong, Zhiwei, Yiu, Vor, Liu, Guichun, He, Jinwu, Zhao, Ruoping, Peng, Yanqiong & Li, Xueyan, 2021, Three new species of Lamprigera Motschulsky (Coleoptera, Lampyridae) from China, with notes on known species, pp. 441-468 in Zootaxa 4950 (3) on pages 449-450, DOI: 10.11646/zootaxa.4950.3.2, http://zenodo.org/record/464996

Lamprigera magnapronotum Dong & Yiu & Liu & He & Zhao & Peng & Li 2021, sp. nov.

Lamprigera magnapronotum Dong & Li, sp. nov. Figs 64–69 Type locality. Huangmaolin Village, Yuanyang County, Honghe Prefecture, Yunnan, China. Type material. Holotype: &male;, Huangmaolin Village, Yuanyang County, Honghe Prefecture, Yunnan, China, 14.VIII.2007, leg. Xue-Yan Li & Qin-Bai Hou (KIZ). Paratypes, one &male;, same data as holotype (KIZ) (Lg18). Additional material examined. One &female;, Menglun Botanical Garden, Xishuangbanna Prefecture, Yunnan, China, 13.VIII.2015, leg. Xue-Yan Li & Zhi-Wei Dong (Lg17-F); One larva, Ailao Mountain, Xinping County, Yuxi City, Yunnan, China, V.2016, leg. Lu Qiu (Lg5-L). Diagnosis. This species has short oblong body (BW/BL approximate 0.63). It has large pronotum with brown ridges at margin and two transparent windows at the anterior top, and its pronotum is wider than elytra. Description. Male (Figs 64–66). Body short oblong. BL: 17.5 mm; BW: 11 mm; BW/BL approximate 0.63. Coloration (Figs 64–66): head black; pronotum with the pentagonal pronotal disc black and other part light yellow; scutellum dark brown; elytra uniformly dark brown with light brown pilosity; legs with tibiae and tarsi brown to dark brown; abdominal ventrites I-V brown to dark brown, ventrites VI-VII yellow-brown. Head. Large because of big compound eyes; PW/GHW = 2.15; compound eyes kidney-shaped in lateral view and almost contiguous ventrally. Antennae clavate, short, slightly longer than the diameter of a compound eye, a little exceeding the front edge of pronotum in transverse condition, thickly hirsute, first antennomere cylindrical and as long as second, second narrower, 3-10segments triangular, last antennomere bifurcate apically. Mandibles curved, slender and sharply pointed; maxillary palp 5-segmented, apical segment circular; labial palp bi-segmented. Thorax. Pronotum (Fig. 66) semi-elliptical (PW/PL =1.91), surface clad with short, yellow-brown setae; widest at base; posterior margin flat; having two translucent windows only at the frontal edge, posterior angles rounded, wider than body width. Scutellum small, rhombus. Abdomen. Abdominal surface clad with short setae. Pygidium flat in the middle of posterior edge. Ventrite VII semi-circular. (67–69). Male genitalia (Figs 67–69). Aedeagus sheath 1.84 mm long. Aedeagus 2.22 mm long, well-sclerotised. Basal piece oblong and smooth, shorter than parameres. Medial lobe uniformly strong, a little longer than parameres. Parameres strong, becoming gradually thicker from the bottom until 1/2, and then tapering from 1/2, with a sharply pointed end. Females. According to pairwise nucleotide distances of COI, one female population from Manglu (Yunnan) (Lg 17-F) (with a distance of 0.008 to type population) is identified as the same species. Immatures. According to pairwise nucleotide distances of COI, one larval population from Xinping (Yunnan) (Lg 5-L) (with a distance of 0.043 to type population) is identified as the same species. Etymology. The species name magnapronotum is a combination of the Latin word magna meaning huge and pronotum, denoting its huge pronotum. Distribution. China: Yunnan: Yuanyang, Mengla, Xinping. Remarks. This species can be separated from nine species previously reported or newly described here based on type specimens (L. minor, L. dorsalis, L. taimoshana, L. yunnana, L. lutosipennis, L. altcola, L. marussii, L. luquanensis) or original description (L. angustior) (Fairmaire, 1886; Pic, 1955) by its pronotum with two translucent windows only at the frontal edge with a costae between two windows and the remaining area dark brown (Fig. 66). It can be separated from L. tenebrosa which has yellow brown elytra (Fig. 22). It has dark brown femur, which can separate it from L. morator, L. nepalensis, L. nitidicollis, L. tardus with yellow brown femurs (Figs 17, 20, 26, 29). It has brown thoracic venters and ventrites I–VII, which can separate it from L. boyei with yellow venters (Fig. 14). It can be separated from L. nitens (Olivier, 1885) by the last two reddish ventrites of the latter. It has brown scutellum with round apex (Fig. 64), which can be used to separate from L. scutatus (russet scutellum with narrow apex) (Fairmaire, 1897b), L. crassus (pitchy scutellum) (Gorham, 1880) and L. diffinis (Figs 31, 48: scutellum with narrow apex).Published as part of Dong, Zhiwei, Yiu, Vor, Liu, Guichun, He, Jinwu, Zhao, Ruoping, Peng, Yanqiong & Li, Xueyan, 2021, Three new species of Lamprigera Motschulsky (Coleoptera, Lampyridae) from China, with notes on known species, pp. 441-468 in Zootaxa 4950 (3) on pages 455-457, DOI: 10.11646/zootaxa.4950.3.2, http://zenodo.org/record/464996