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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
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    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
    American Association for the Advancement of Science (AAAS) ; 2019
    In:  Science Vol. 364, No. 6446 ( 2019-06-21)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 364, No. 6446 ( 2019-06-21)
    Abstract: The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aav6202
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2019
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 3
    Online Resource
    Online Resource
    Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies
    Springer Science and Business Media LLC ; 2015
    In:  Nature Communications Vol. 6, No. 1 ( 2015-09-10)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2015-09-10)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/ncomms9212
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2553671-0
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  • 4
    Online Resource
    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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  • 5
    Online Resource
    Online Resource
    Generation of biallelic knock-out sheep via gene-editing and somatic cell nuclear transfer
    Springer Science and Business Media LLC ; 2016
    In:  Scientific Reports Vol. 6, No. 1 ( 2016-09-22)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-09-22)
    Abstract: Transgenic sheep can be used to achieve genetic improvements in breeds and as an important large-animal model for biomedical research. In this study, we generated a TALEN plasmid specific for ovine MSTN and transfected it into fetal fibroblast cells of STH sheep. MSTN biallelic-KO somatic cells were selected as nuclear donor cells for SCNT. In total, cloned embryos were transferred into 37 recipient gilts, 28 (75.7%) becoming pregnant and 15 delivering, resulting in 23 lambs, 12 of which were alive. Mutations in the lambs were verified via sequencing and T7EI assay and the gene mutation site was consistent with that in the donor cells. Off-target analysis was performed and no off-target mutations were detected. MSTN KO affected the mRNA expression of MSTN relative genes. The growth curve for the resulting sheep suggested that MSTN KO caused a remarkable increase in body weight compared with those of wild-type sheep. Histological analyses revealed that MSTN KO resulted in muscle fiber hypertrophy. These findings demonstrate the successful generation of MSTN biallelic-KO STH sheep via gene editing in somatic cells using TALEN technology and SCNT. These MSTN mutant sheep developed and grew normally and exhibited increased body weight and muscle growth.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/srep33675
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2615211-3
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  • 6
    Online Resource
    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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