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  • 1
    Online Resource
    Online Resource
    Multiple origins of bioluminescence in beetles and evolution of luciferase function
    Oxford University Press (OUP) ; 2024
    In:  Molecular Biology and Evolution
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP)
    Abstract: Bioluminescence in beetles has long fascinated biologists, with diverse applications in biotechnology. To date, however, our understanding of its evolutionary origin and functional variation mechanisms remains poor. To address these questions, we obtained high-quality reference genomes of luminous and non-luminous beetles in six Elateroidea families. We then reconstructed a robust phylogenetic relationship for all luminous families and related non-luminous families. Comparative genomic analyses and biochemical functional experiments suggested that gene evolution within Elateroidea played a crucial role in the origin of bioluminescence, with multiple parallel origins observed in the luminous beetle families. While most luciferase-like proteins exhibited a conserved non-luminous amino acid pattern (TLA346–348) in the luciferin-binding sites, luciferases in the different luminous beetle families showed divergent patterns at these sites (TSA/CCA/CSA/LVA). Comparisons of the structural and enzymatic properties of ancestral, extant, and site-directed mutant luciferases further reinforced the important role of these sites in the trade-off between acyl-CoA synthetase and luciferase activities. Furthermore, the evolution of bioluminescent color demonstrated a tendency towards hypsochromic shifts and variations among the luminous families. Taken together, our results revealed multiple parallel origins of bioluminescence and functional divergence within the beetle bioluminescent system.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msad287
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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  • 2
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    Online Resource
    Genome size variation in butterflies (Insecta, Lepidotera, Papilionoidea): a thorough phylogenetic comparison
    Wiley ; 2020
    In:  Systematic Entomology Vol. 45, No. 3 ( 2020-07), p. 571-582
    Details
    In: Systematic Entomology, Wiley, Vol. 45, No. 3 ( 2020-07), p. 571-582
    Abstract: Butterflies have been of great interest to naturalists for centuries, and the study of butterflies has been an integral part of ecology and evolution ever since Darwin proposed his theory of natural selection in 1859. There are 〉  18 000 butterfly species worldwide, showing great diversity in morphological traits and ecological niches. Compared with butterfly diversity, however, patterns of genome size variation in butterflies remain poorly understood, especially in a phylogenetic context. Here, we sequenced and assembled the mitogenomes of 68 butterflies and measured the genome sizes ( C ‐values) of 67 of them. We also assembled 10 mitogenomes using reads from GenBank. Among the assembled 78 mitogenomes, those from 59 species, 23 genera and one subfamily are reported for the first time. Combining with published data of mitogenomes and genome size, we explored the patterns in genome size variation for 106 butterfly species in a phylogenetic context based on analyses of mitogenomes from 264 species covering six families. Our results show that the genome size of butterflies has a 6.4‐fold variation ranging from 0.203 pg (199 Mb) (Nymphalidae: Heliconius xanthocles ) to 1.287 pg (1253 Mb) (Papilionidae: Parnassius orleans ). Within families, the largest variation was found in Papilionidae (5.9‐fold: 0.22–1.29 pg), followed by Nymphalidae (4.8‐fold: 0.2–0.95 pg), Pieridae (4.4‐fold: 0.22–0.97 pg), Hesperiidae (2.2‐fold: 0.3–0.66 pg), Lycaenidae (2.6‐fold: 0.39–1.02 pg) and Rioidinidae (1.8‐fold: 0.48–0.87 pg). Our data also suggest that butterflies have an ancestral genome size of c. 0.5 pg, and some ancestral genome size increase or decrease events along different subfamilies or tribes produce the diversity of genome size variation in diverse butterflies. Our data provide novel insights into patterns of genome size variation in butterflies and are an important reference for future genome sequencing programmes.
    Type of Medium: Online Resource
    ISSN: 0307-6970 , 1365-3113
    URL: Issue
    URL: Article
    DOI: 10.1111/syen.v45.3
    DOI: 10.1111/syen.12417
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020957-5
    SSG: 12
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  • 3
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    Online Resource
    Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies
    Springer Science and Business Media LLC ; 2020
    In:  Scientific Reports Vol. 10, No. 1 ( 2020-09-28)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-09-28)
    Abstract: Fireflies are among the most charismatic insects for their spectacular bioluminescence, but the origin and evolution of bioluminescence remain elusive. Especially, the genic basis of luciferin ( d -luciferin) biosynthesis and light patterns is largely unknown. Here, we present the high-quality reference genomes of two fireflies Lamprigera yunnana (1053 Mb) and Abscondita terminalis (501 Mb) with great differences in both morphology and luminous behavior. We sequenced the transcriptomes and proteomes of luminous organs of two species. We created the CRISPR/Cas9-induced mutants of Abdominal B gene without luminous organs in the larvae of A. terminalis and sequenced the transcriptomes of mutants and wild-types. Combining gene expression analyses with comparative genomics, we propose a more complete luciferin synthesis pathway, and confirm the convergent evolution of bioluminescence in insects. Using experiments, the function of the firefly acyl-CoA thioesterase (ACOT1) to convert l -luciferin to d -luciferin was validated for the first time. Comparisons of three-dimension reconstruction of luminous organs and their differentially expressed genes among two species suggest that two positive genes in the calcium signaling pathway and structural difference of luminous organs may play an important role in the evolution of flash pattern. Altogether, our results provide important resources for further exploring bioluminescence in insects.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-020-72900-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2615211-3
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  • 4
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    Online Resource
    Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis
    Oxford University Press (OUP) ; 2019
    In:  GigaScience Vol. 8, No. 11 ( 2019-11-01)
    Details
    In: GigaScience, Oxford University Press (OUP), Vol. 8, No. 11 ( 2019-11-01)
    Abstract: Papilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies. Findings We obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69–36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period. Conclusions We present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C–based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.
    Type of Medium: Online Resource
    ISSN: 2047-217X
    URL: Article
    DOI: 10.1093/gigascience/giz128
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2708999-X
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  • 5
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    Online Resource
    Chromosome‐level reference genome assembly and gene editing of the dead‐leaf butterfly Kallima inachus
    Wiley ; 2020
    In:  Molecular Ecology Resources Vol. 20, No. 4 ( 2020-07), p. 1080-1092
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 20, No. 4 ( 2020-07), p. 1080-1092
    Abstract: The leaf resemblance of Kallima (Nymphalidae) butterflies is an important ecological adaptive mechanism that increases their survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Here, we determined the karyotype ( n  = 31) of the dead‐leaf butterfly Kallima inachus , and generated a high‐quality, chromosome‐level assembly (568.92 Mb; contig N50: 19.20 Mb). We also identified candidate Z and W chromosomes. To our knowledge, this is the first study to report on these aspects of this species. In the assembled genome, 15,309 protein‐coding genes and 49.86% repeat elements were annotated. Phylogenetic analysis showed that K. inachus diverged from Melitaea cinxia (no leaf resemblance), both of which are in Nymphalinae, around 40 million years ago. Demographic analysis indicated that the effective population size of K. inachus decreased during the last interglacial period in the Pleistocene. The wings of adults with the pigmentary gene ebony knocked out using CRISPR/Cas9 showed phenotypes in which the orange dorsal region and entire ventral surface darkened, suggesting its vital role in the ecological adaption of dead‐leaf butterflies. Our results provide important genome resources for investigating the genetic mechanism underlying protective resemblance in dead‐leaf butterflies and insights into the molecular basis of protective coloration.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v20.4
    DOI: 10.1111/1755-0998.13185
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2406833-0
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  • 6
    Online Resource
    Online Resource
    Complete mitochondrial genome of Pectocera sp. (Elateridae: Dendrometrinae: Oxynopterini) and its phylogenetic implications
    Wiley ; 2022
    In:  Archives of Insect Biochemistry and Physiology Vol. 111, No. 1 ( 2022-09)
    Details
    In: Archives of Insect Biochemistry and Physiology, Wiley, Vol. 111, No. 1 ( 2022-09)
    Abstract: The mitogenome of Pectocera sp. (Elateridae: Dendrometrinae: Oxynopterini) was sequenced, annotated, and analyzed, and the results show that the mitogenome is highly conserved in gene number and order as those of most beetle mitogenomes. Comparative genomic analyses showed a high degree of feature similarity among the mitogenomes of Pectocera sp. and other click beetles, such as base composition and AT‐bias. Phylogenetic analyses based on 13 PCGs and two rRNA genes ( rrnS and rrnL ) indicated that Pectocera sp. and Campsosternus auratus were grouped together in Oxynopterini with high support. The findings recovered the monophyly of the four subfamilies (Cardiophorinae, Agrypninae, Elaterinae, and Dendrometrinae), and confirmed the phylogenetic position of Pectocera in the tribe Oxynopterini of Dendrometrinae.
    Type of Medium: Online Resource
    ISSN: 0739-4462 , 1520-6327
    URL: Issue
    URL: Article
    DOI: 10.1002/arch.v111.1
    DOI: 10.1002/arch.21957
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1496071-0
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  • 7
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    Online Resource
    Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus
    Springer Science and Business Media LLC ; 2021
    In:  BMC Genomics Vol. 22, No. 1 ( 2021-02-17)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-02-17)
    Abstract: Insect body coloration often functions as camouflage to survive from predators or mate selection. Transportation of pigment precursors or related metabolites from cytoplasm to subcellular pigment granules is one of the key steps in insect pigmentation and usually executed via such transporter proteins as the ATP-binding cassette (ABC) transmembrane transporters and small G-proteins (e.g. Rab protein). However, little is known about the copy numbers of pigment transporter genes in the butterfly genomes and about the roles of pigment transporters in the development of swallowtail butterflies. Results Here, we have identified 56 ABC transporters and 58 Rab members in the genome of swallowtail butterfly Papilio xuthus . This is the first case of genome-wide gene copy number identification of ABC transporters in swallowtail butterflies and Rab family in lepidopteran insects. Aiming to investigate the contribution of the five genes which are orthologous to well-studied pigment transporters (ABCG: white , scarlet , brown and ok ; Rab: lightoid ) of fruit fly or silkworm during the development of swallowtail butterflies, we performed CRISPR/Cas9 gene-editing of these genes using P. xuthus as a model and sequenced the transcriptomes of their morphological mutants. Our results indicate that the disruption of each gene produced mutated phenotypes in the colors of larvae (cuticle, testis) and/or adult eyes in G0 individuals but have no effect on wing color. The transcriptomic data demonstrated that mutations induced by CRISPR/Cas9 can lead to the accumulation of abnormal transcripts and the decrease or dosage compensation of normal transcripts at gene expression level. Comparative transcriptomes revealed 606 ~ 772 differentially expressed genes (DEGs) in the mutants of four ABCG transporters and 1443 DEGs in the mutants of lightoid . GO and KEGG enrichment analysis showed that DEGs in ABCG transporter mutants enriched to the oxidoreductase activity, heme binding, iron ion binding process possibly related to the color display, and DEGs in lightoid mutants are enriched in glycoprotein binding and protein kinases. Conclusions Our data indicated these transporter proteins play an important role in body color of P. xuthus . Our study provides new insights into the function of ABC transporters and small G-proteins in the morphological development of butterflies.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-021-07400-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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