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1. The T2T Genome of the Domesticated Silkworm Bombyx mori.

Author

Li, Wan-Shun, Xiao, Ying-Dan, Liu, Jian-Qiu, Li, Sheng-Long, Chen, Yue, Xu, Ya-Jing, Yang, Xue, Wang, Yan-Jue, Li, Zhi-Qing, Xia, Qing-You, and Mita, Kazuei

Subjects
SILKWORMS, BASE pairs, CHROMOSOMES, NUCLEOTIDE sequencing, GENOMES
Abstract

Genome sequences contain the fundamental genetic information that largely determines the biology of a species. Over the past 20 years, advancements in high-throughput sequencing technologies and bioinformatics tools have matured, facilitating genome assembly and ushering in the telomere-to-telomere (T2T) era. Bombyx mori is renowned as a silk-producing insect and serves as an important model organism extensively studied across various fields of biology. In this study, we present the first assembled T2T genome by integrating HiFi, ultra-long ONT, NGS, and Hi-C data. This assembly comprises 450,267,439 base pairs from 28 chromosomes and includes annotations for a total of 18,253 protein-coding genes. A completeness evaluation revealed that 99.1% of conserved single-copy genes were included, as determined by a BUSCO analysis. Furthermore, the consensus quality (QV) assessed through Merqury was recorded at 59.88. The proportion of repeat sequence achieved 60.77%, marking it as the highest reported value for B. mori to date. In comparison to previously published genomes, our assembly offers a more complete and higher quality representation, particularly concerning highly homologous tandem regions such as telomeres, rDNA clusters, and Gr family regions. Furthermore, our extensive experience in genome assembly, including sample preparation experience and assembly strategies to reduce complexity, will provide valuable references for other species aiming to achieve their own T2T genome assemblies. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Proteotranscriptomic analyses of the midgut and Malpighian tubules after a sublethal concentration of Cry1Ab exposure on Spodoptera litura.

Author

Xu, Ya‐Jing, Zhang, Yu‐Ning, Xue‐Yang, Hao, Shao‐Peng, Wang, Yan‐Jue, Yang, Xiao‐Xue, Shen, Ya‐Qin, Su, Qing, Xiao, Ying Dan, Liu, Jian‐Qiu, Li, Wan‐Shun, He, Qi‐Hua, Chen, Yue, Wang, Li‐Ling, Guo, Hui‐Zhen, Xia, Qing‐You, and Mita, Kazuei

Subjects
SPODOPTERA littoralis, GENE expression, PROTEIN receptors, OXIDATIVE phosphorylation, RNA sequencing, RIBOSOMAL proteins, RIBOSOMES
Abstract

BACKGROUND: Cry1Ab has emerged as a bio‐insecticide to control Spodoptera litura (Lepidoptera: Noctuidae). However, the sublethal effects of Cry1Ab on the physiological changes and molecular level of S. litura have not been well documented. Our aims in this study were to assess the sublethal effect of Cry1Ab on S. litura, including midgut and Malpighian tubules as targets. RESULTS: After sublethal Cry1Ab exposure, distinct histological alterations were mainly observed in the midgut. Furthermore, the results of comparative RNA sequencing and tandem mass tag‐based proteomics showed that, in the midgut, most differential expression genes (DEGs) were up‐regulated and significantly enriched in the serine protease activity pathway, and up‐regulated differential expression proteins (DEPs) were mainly associated with the oxidative phosphorylation pathway, whereas the down‐regulated involved in the ribosome pathways. In the Malpighian tubules, DEGs and DEPs were significantly enriched in the ribosome pathway. We proposed that ribosome may act as a universal target in energy metabolism with other pathways via the results of protein–protein interaction analysis. Further, by verification of the mRNA expression of some Cry protein receptor and detoxification genes after Cry1Ab treatment, it was suggested that the ribosomal proteins (RPs) possibly participate in influencing the Bt‐resistance of S. litura larvae under sublethal Cry1Ab exposure. CONCLUSION: Under sublethal Cry1Ab exposure, the midgut of S. litura was damaged, and the proteotranscriptomic analysis elucidated that Cry1Ab disrupted the energy homeostasis of larvae. Furthermore, we emphasized the potential role of ribosomes in sublethal Cry1Ab exposure. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Molecular Evolution of Lepidopteran Silk Proteins: Insights from the Ghost Moth, Hepialus californicus

Author

Collin, Matthew A., Mita, Kazuei, Sehnal, Frantisek, and Hayashi, Cheryl Y.

Subjects
Life Sciences, Animal Genetics and Genomics, Plant Genetics & Genomics, Plant Sciences, Microbiology, Evolutionary Biology, Cell Biology, Lepidoptera, Trichoptera, Silk, Fibroin, cDNA, Gene tree, Purifying selection
Abstract

Silk production has independently evolved in numerous arthropod lineages, such as Lepidoptera, the moths and butterflies. Lepidopteran larvae (caterpillars) synthesize silk proteins in modified salivary glands and spin silk fibers into protective tunnels, escape lines, and pupation cocoons. Molecular sequence data for these proteins are necessary to determine critical features of their function and evolution. To this end, we constructed an expression library from the silk glands of the ghost moth, Hepialus californicus, and characterized light chain fibroin and heavy chain fibroin gene transcripts. The predicted H. californicus silk fibroins share many elements with other lepidopteran and trichopteran fibroins, such as conserved placements of cysteine, aromatic, and polar amino acid residues. Further comparative analyses were performed to determine site-specific signatures of selection and to assess whether fibroin genes are informative as phylogenetic markers. We found that purifying selection has constrained mutation within the fibroins and that light chain fibroin is a promising molecular marker. Thus, by characterizing the H. californicus fibroins, we identified key functional amino acids and gained insight into the evolutionary processes that have shaped these adaptive molecules.

Published
2010

15. Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori

Author

Guo, Huizhen, Cheng, Tingcai, Chen, Zhiwei, Jiang, Liang, Guo, Youbing, Liu, Jianqiu, Li, Shenglong, Taniai, Kiyoko, Asaoka, Kiyoshi, Kadono-Okuda, Keiko, Arunkumar, Kallare P., Wu, Jiaqi, Kishino, Hirohisa, Zhang, Huijie, Seth, Rakesh K., Gopinathan, Karumathil P., Montagné, Nicolas, Jacquin-Joly, Emmanuelle, Goldsmith, Marian R., Xia, Qingyou, and Mita, Kazuei

Published
2017
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20. Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

Author

Cheng, Tingcai, Wu, Jiaqi, Wu, Yuqian, Chilukuri, Rajendra V., Huang, Lihua, Yamamoto, Kohji, Feng, Li, Li, Wanshun, Chen, Zhiwei, Guo, Huizhen, Liu, Jianqiu, Li, Shenglong, Wang, Xiaoxiao, Peng, Li, Liu, Duolian, Guo, Youbing, Fu, Bohua, Li, Zhiqing, Liu, Chun, Chen, Yuhui, Tomar, Archana, Hilliou, Frederique, Montagné, Nicolas, Jacquin-Joly, Emmanuelle, d’Alençon, Emmanuelle, Seth, Rakesh K., Bhatnagar, Raj K., Jouraku, Akiya, Shiotsuki, Takahiro, Kadono-Okuda, Keiko, Promboon, Amornrat, Smagghe, Guy, Arunkumar, Kallare P., Kishino, Hirohisa, Goldsmith, Marian R., Feng, Qili, Xia, Qingyou, and Mita, Kazuei

Published
2017
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23. Identification of novel genes expressed highly and selectively in the corpora allata of the silkworm, Bombyx mori(Lepidoptera: Bombycidae)

Author

Homma, Yuri, Mita, Kazuei, Nakamura, Yuki, Namiki, Toshiki, Noda, Hiroaki, Shinoda, Tetsuro, and Togawa, Toru

Abstract

Juvenile hormone (JH) has crucial roles in insect physiology, including development, reproduction, and polyphenism. JH is synthesized in the corpora allata (CA) from acetyl-CoA through 13 enzymatic steps, which can be divided into the early mevalonate pathway and the late JH branch pathway. Genes for these 13 enzymes have been identified in several insect species, although the three genes for the first three steps in the late pathway are unclear in many insect species. Information about the regulatory mechanism of JH biosynthesis in the CA has been accumulated in previous researches, but the process is not fully understood. In this study, we identified two genes that are expressed highly and selectively in the CA of the silkworm, Bombyx mori(L.) (Lepidoptera: Bombycidae), through the screening using EST library, DNA microarray, and qRT-PCR analyses. These genes showed developmental expression patterns that correlate well with the fluctuation pattern of JH biosynthetic activity in the CA, suggesting important roles in JH biosynthesis or its regulation.

Published
2024
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45. Positional cloning of a gene responsible for the cts mutation of the silkworm, Bombyx mori

Author

Ito, Katsuhiko, Kidokoro, Kurako, Katsuma, Susumu, Shimada, Toru, Yamamoto, Kimiko, Mita, Kazuei, and Kadono-Okuda, Keiko

Subjects
Gene mutations -- Identification and classification, Silkworms -- Genetic aspects, DNA testing -- Research, Evolutionary genetics -- Research, Biological sciences
Abstract

The larval head cuticle and anal plates of the silkworm mutant cheek and tail spot (cts) have chocolate-colored spots, unlike the entirely white appearance of the wild-type (WT) strain. We report the identification and characterization of the gene responsible for the cts mutation. Positional cloning revealed a cts candidate on chromosome 16, designated BmMFS, based on the high similarity of the deduced amino acid sequence between the candidate gene from the WT strain and the major facilitator superfamily (MFS) protein. BmMFS likely encodes a membrane protein with 11 putative transmembrane domains, while the putative structure deduced from the cts-type allele possesses only 10-pass transmembrane domains owing to a deletion in its coding region. Quantitative RT-PCR analysis showed that BmMFS mRNA was strongly expressed in the integument of the head and tail, where the cts phenotype is observed; expression markedly increased at the molting and newly ecdysed stages. These results indicate that the novel BmMFS gene is cts and the membrane structure of its protein accounts for the cts phenotype. These expression profiles and the cts phenotype are quite similar to those of melanin-related genes, such as Bmyellow-e and Bm-iAANAT, suggesting that BmMFS is involved in the melanin synthesis pathway. Key words: Bombyx mori, cts mutant, positional cloning, melanin, major facilitator superfamily (MFS). La cuticule de la tete et les plaques anales chez les larves du mutant cheek and tail spot (cts) du vers a soie presentent des taches de couleur chocolat contrairement au type sauvage (WT) qui est entierement blanc. Les auteurs rapportent l'identification et la caracterisation du gene responsable de la mutation cts. Le clonage positionnel a permis d'identifier un gene candidat sur le chromosome 16; celui-ci a ete nomme BmMFS en raison de la grande similarite entre la sequence peptidique predite chez le WT et les proteines de la superfamille MFS (' major facilitator superfamily '). Le gene BmMFS code vraisemblablement pour une proteine membranaire avec 11 domaines transmembranaires, tandis que la structure predite pour l'allele cts n'en presenterait que 10 en raison d'une deletion au sein de la region codante. Des analyses RT-PCR quantitatives ont revele que l'ARNm de BmMFS est exprime fortement au sein du tegument de la tete et de la queue, la ou le phenotype s'observe. L'expression augmente de maniere importante au cours de la mue et des stades qui en resultent. Ces resultats indiquent que le gene BmMFS correspondrait a cts et que la structure membranaire de sa proteine expliquerait le phenotype mutant cts. Ces profils d' expression et le phenotype cts sont tres semblables a ceux des genes associes a la melanine comme Bmyellow-e et Bm-iAANAT, ce qui suggere que BmMFS serait implique dans le sentier de synthese de la melanine. Mots-cles : Bombyx mori, mutant cts, clonage positionnel, melanine, superfamille MFS. [Traduit par la Redaction], Introduction Many lepidopteran insects show body color variations. The high phenotypic diversity observed in butterfly wings and larval body patterns offers an opportunity to study adaptive morphological evolution (Ferguson et [...]

Published
2012
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