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Lu K, Pan Y, Shen J, Yang L, Zhan C, Liang S, Tai S, Wan L, Li T, Cheng T, Ma B, Pan G, He N, Lu C, Westhof E, Xiang Z, Han MJ, Tong X, Dai F. SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data. Nucleic Acids Res 2024; 52:D1024-D1032. [PMID: 37941143 PMCID: PMC10767832 DOI: 10.1093/nar/gkad956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.
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Affiliation(s)
- Kunpeng Lu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yifei Pan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jianghong Shen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Lin Yang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Chengyu Zhan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Shubo Liang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | | | - Linrong Wan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Tingcai Cheng
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Bi Ma
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Ningjia He
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Eric Westhof
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Zhonghuai Xiang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
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Hoshizaki S. Ontogenetic progression of individual head size in the larvae of the beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): catch-up growth within stages and per-stage growth rate changes across stages. PeerJ 2023; 11:e15451. [PMID: 37273541 PMCID: PMC10239228 DOI: 10.7717/peerj.15451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
The ontogenetic progression of insect larval head size has received much attention due to its fundamental and practical importance. However, although previous studies have analyzed the population mean head size, such an approach may not be appropriate for developmental studies of larval head sizes when the trajectory of individual head size growth is correlated with pre-molt head size and developmental stage. Additionally, there is covariation between the head and body sizes; however, few studies have compared the ontogenetic progression of individual head sizes with that of individual body sizes. In this investigation, the per-stage growth rates (PSGRs) for head width (HW) and cubic-rooted body mass at the beginning of each instar (body size, BS) were assessed in Trypoxylus dichotomus. Linear models were used to test the size- and instar-dependence of the ontogenetic progression of individual HW and BS. The individual PSGRs of the HW (iPSGRH) and BS (iPSGRB) were then compared. In addition, the allometric relationship between HW and BS was examined. The iPSGRH was negatively correlated with the pre-molt HW at every instar (i.e., head catch-up growth). Furthermore, the mean iPSGRH at L2 was relatively higher than that at L1 when the pre-molt HW was used as covariate in the analysis (i.e., instar-effect), whereas the mean iPSGRH decreased ontogenetically. The iPSGRB showed catch-up growth and instar-effects similar to those of iPSGRH; however, iPSGRH was found to be lower than iPSGRB. Due to the differences between the PSGRs for the larval head and body, the larval head size showed negative ontogenetic allometry against body size.
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Tong X, Han MJ, Lu K, Tai S, Liang S, Liu Y, Hu H, Shen J, Long A, Zhan C, Ding X, Liu S, Gao Q, Zhang B, Zhou L, Tan D, Yuan Y, Guo N, Li YH, Wu Z, Liu L, Li C, Lu Y, Gai T, Zhang Y, Yang R, Qian H, Liu Y, Luo J, Zheng L, Lou J, Peng Y, Zuo W, Song J, He S, Wu S, Zou Y, Zhou L, Cheng L, Tang Y, Cheng G, Yuan L, He W, Xu J, Fu T, Xiao Y, Lei T, Xu A, Yin Y, Wang J, Monteiro A, Westhof E, Lu C, Tian Z, Wang W, Xiang Z, Dai F. High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation. Nat Commun 2022; 13:5619. [PMID: 36153338 PMCID: PMC9509368 DOI: 10.1038/s41467-022-33366-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.
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Kamiyama T, Niwa R. Transcriptional Regulators of Ecdysteroid Biosynthetic Enzymes and Their Roles in Insect Development. Front Physiol 2022; 13:823418. [PMID: 35211033 PMCID: PMC8863297 DOI: 10.3389/fphys.2022.823418] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Steroid hormones are responsible for coordinating many aspects of biological processes in most multicellular organisms, including insects. Ecdysteroid, the principal insect steroid hormone, is biosynthesized from dietary cholesterol or plant sterols. In the last 20 years, a number of ecdysteroidogenic enzymes, including Noppera-bo, Neverland, Shroud, Spook/Spookier, Cyp6t3, Phantom, Disembodied, Shadow, and Shade, have been identified and characterized in molecular genetic studies using the fruit fly Drosophila melanogaster. These enzymes are encoded by genes collectively called the Halloween genes. The transcriptional regulatory network, governed by multiple regulators of transcription, chromatin remodeling, and endoreplication, has been shown to be essential for the spatiotemporal expression control of Halloween genes in D. melanogaster. In this review, we summarize the latest information on transcriptional regulators that are crucial for controlling the expression of ecdysteroid biosynthetic enzymes and their roles in insect development.
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Affiliation(s)
- Takumi Kamiyama
- College of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
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Hombría JCG, García-Ferrés M, Sánchez-Higueras C. Anterior Hox Genes and the Process of Cephalization. Front Cell Dev Biol 2021; 9:718175. [PMID: 34422836 PMCID: PMC8374599 DOI: 10.3389/fcell.2021.718175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
During evolution, bilateral animals have experienced a progressive process of cephalization with the anterior concentration of nervous tissue, sensory organs and the appearance of dedicated feeding structures surrounding the mouth. Cephalization has been achieved by the specialization of the unsegmented anterior end of the body (the acron) and the sequential recruitment to the head of adjacent anterior segments. Here we review the key developmental contribution of Hox1-5 genes to the formation of cephalic structures in vertebrates and arthropods and discuss how this evolved. The appearance of Hox cephalic genes preceded the evolution of a highly specialized head in both groups, indicating that Hox gene involvement in the control of cephalic structures was acquired independently during the evolution of vertebrates and invertebrates to regulate the genes required for head innovation.
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Affiliation(s)
- James C-G Hombría
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Mar García-Ferrés
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Carlos Sánchez-Higueras
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
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