The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

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Dataset of de novo assembly and functional annotation of the transcriptome of certain developmental stages of coconut rhinoceros beetle, Oryctes rhinoceros L.

Data in Brief ◽

10.1016/j.dib.2019.105036 ◽

2020 ◽

Vol 28 ◽

pp. 105036

Author(s):

Kumar Arvind ◽

M.K. Rajesh ◽

A. Josephrajkumar ◽

Tony Grace

Keyword(s):

De Novo Assembly ◽

Functional Annotation ◽

Developmental Stages ◽

De Novo ◽

Oryctes Rhinoceros ◽

Rhinoceros Beetle

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De novo assembly and annotation of the mangrove cricket genome

BMC Research Notes ◽

10.1186/s13104-021-05798-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Aya Satoh ◽

Miwako Takasu ◽

Kentaro Yano ◽

Yohey Terai

Keyword(s):

De Novo Assembly ◽

Molecular Mechanisms ◽

De Novo ◽

Draft Genome ◽

Swissprot Database ◽

Data Description ◽

Pfam Database ◽

Molecular Studies ◽

Free Running ◽

Endogenous Activity

Abstract Objectives The mangrove cricket, Apteronemobius asahinai, shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a free-running rhythm with a period of ~ 12.4 h [the circatidal rhythm]). Little is known about the molecular mechanisms underlying the circatidal rhythm. We present the draft genome of the mangrove cricket to facilitate future molecular studies of the molecular mechanisms behind this rhythm. Data description The draft genome contains 151,060 scaffolds with a total length of 1.68 Gb (N50: 27 kb) and 92% BUSCO completeness. We obtained 28,831 predicted genes, of which 19,896 (69%) were successfully annotated using at least one of two databases (UniProtKB/SwissProt database and Pfam database).

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The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus

Genome Biology and Evolution ◽

10.1093/gbe/evz141 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1965-1970 ◽

Cited By ~ 7

Author(s):

Nikola Palevich ◽

Paul H Maclean ◽

Abdul Baten ◽

Richard W Scott ◽

David M Leathwick

Keyword(s):

Genome Sequence ◽

Molecular Mechanisms ◽

De Novo ◽

Sequence Data ◽

Animal Health ◽

Draft Genome ◽

Whole Genome Sequence ◽

Parasitic Nematodes ◽

Hybrid Assembly ◽

Genetic Structures

Abstract Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites. A de novo hybrid assembly was generated from PCR-free whole genome sequence data, resulting in a chromosome-level assembly that is 465 Mb in size encoding 22,341 genes. The genome sequence presented here is consistent with the genome architecture of the existing Haemonchus species and is a valuable resource for future studies regarding population genetic structures of parasitic nematodes. Additionally, comparative pan-genomics with other species of economically important parasitic nematodes have revealed highly open genomes and strong collinearities within the phylum Nematoda.

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The islet ghrelin cell

Journal of Molecular Endocrinology ◽

10.1530/jme-13-0122 ◽

2013 ◽

Vol 52 (1) ◽

pp. R35-R49 ◽

Cited By ~ 52

Author(s):

Nils Wierup ◽

Frank Sundler ◽

R Scott Heller

Keyword(s):

Molecular Mechanisms ◽

Developmental Stages ◽

Developmental Regulation ◽

Genetic Regulation ◽

Cell Types ◽

Human Islets ◽

Histochemical Staining ◽

Pancreatic Tumours ◽

Age Related ◽

Staining Methods

The islets of Langerhans are key regulators of glucose homeostasis and have been known as a structure for almost one and a half centuries. During the twentieth century several different cell types were described in the islets of different species and at different developmental stages. Six cell types with identified hormonal product have been described so far by the use of histochemical staining methods, transmission electron microscopy, and immunohistochemistry. Thus, glucagon-producing α-cells, insulin-producing β-cells, somatostatin-producing δ-cells, pancreatic polypeptide-producing PP-cells, serotonin-producing enterochromaffin-cells, and gastrin-producing G-cells have all been found in the mammalian pancreas at least at some developmental stage. Species differences are at hand and age-related differences are also to be considered. Eleven years ago a novel cell type, the ghrelin cell, was discovered in the human islets. Subsequent studies have shown the presence of islet ghrelin cells in several animals, including mouse, rat, gerbils, and fish. The developmental regulation of ghrelin cells in the islets of mice has gained a lot of interest and several studies have added important pieces to the puzzle of molecular mechanisms and the genetic regulation that lead to differentiation into mature ghrelin cells. A body of evidence has shown that ghrelin is an insulinostatic hormone, and the potential for blockade of ghrelin signalling as a therapeutic avenue for type 2 diabetes is intriguing. Furthermore, ghrelin-expressing pancreatic tumours have been reported and ghrelin needs to be taken into account when diagnosing pancreatic tumours. In this review article, we summarise the knowledge about islet ghrelin cells obtained so far.

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Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

Journal of Insect Science ◽

10.1093/jisesa/iew053 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Juan Ma ◽

Rongyan Wang ◽

Xiuhua Li ◽

Bo Gao ◽

Shulong Chen

Keyword(s):

Sweet Potato ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Average Length ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Cylas Formicarius ◽

Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

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Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

10.21203/rs.3.rs-216108/v1 ◽

2021 ◽

Author(s):

Lei Shi ◽

Yuan Shen ◽

Yuhao Chi

Keyword(s):

Flower Development ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Floral Scent ◽

Expression Profiles ◽

Lonicera Japonica ◽

Biosynthesis Pathway ◽

Terpenoid Biosynthesis ◽

Genes Encoding

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica. The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24, SOC1, AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica. In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica, which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica.

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RNA-Seq de Novo Assembly and Differential Transcriptome Analysis of Chaga (Inonotus obliquus) Cultured with Different Betulin Sources and the Regulation of Genes Involved in Terpenoid Biosynthesis

International Journal of Molecular Sciences ◽

10.3390/ijms20184334 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4334 ◽

Cited By ~ 1

Author(s):

Fradj ◽

Gonçalves dos Santos ◽

de Montigny ◽

Awwad ◽

Boumghar ◽

...

Keyword(s):

Native American ◽

De Novo Assembly ◽

Molecular Mechanisms ◽

De Novo ◽

Gene Prediction ◽

Bioactive Molecules ◽

Birch Bark ◽

Terpenoid Biosynthesis ◽

White Birch ◽

Inonotus Obliquus

Chaga (Inonotus obliquus) is a medicinal fungus used in traditional medicine of Native American and North Eurasian cultures. Several studies have demonstrated the medicinal properties of chaga’s bioactive molecules. For example, several terpenoids (e.g., betulin, betulinic acid and inotodiol) isolated from I. obliquus cells have proven effectiveness in treating different types of tumor cells. However, the molecular mechanisms and regulation underlying the biosynthesis of chaga terpenoids remain unknown. In this study, we report on the optimization of growing conditions for cultured I. obliquus in presence of different betulin sources (e.g., betulin or white birch bark). It was found that better results were obtained for a liquid culture pH 6.2 at 28 °C. In addition, a de novo assembly and characterization of I. obliquus transcriptome in these growth conditions using Illumina technology was performed. A total of 219,288,500 clean reads were generated, allowing for the identification of 20,072 transcripts of I. obliquus including transcripts involved in terpenoid biosynthesis. The differential expression of these genes was confirmed by quantitative-PCR. This study provides new insights on the molecular mechanisms and regulation of I. obliquus terpenoid production. It also contributes useful molecular resources for gene prediction or the development of biotechnologies for the alternative production of terpenoids.

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Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

DNA Research ◽

10.1093/dnares/dsaa006 ◽

2020 ◽

Vol 27 (2) ◽

Author(s):

Pingping Liu ◽

Jie Luo ◽

Qingxia Zheng ◽

Qiansi Chen ◽

Niu Zhai ◽

...

Keyword(s):

Regulatory Networks ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Developmental Process ◽

Pearson Correlation ◽

Molecular Networks ◽

Environmental Perturbations ◽

Carotenoid Metabolism ◽

Gene Modules

Abstract Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

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A high-quality chromosomal genome assembly of Diospyros oleifera Cheng

GigaScience ◽

10.1093/gigascience/giz164 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Yujing Suo ◽

Peng Sun ◽

Huihui Cheng ◽

Weijuan Han ◽

Songfeng Diao ◽

...

Keyword(s):

Molecular Mechanisms ◽

De Novo ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Diospyros Kaki ◽

High Quality ◽

Phylogenetic Tree Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Anthocyanin Pathway

Abstract Background Diospyros oleifera Cheng, of the family Ebenaceae, is an economically important tree. Phylogenetic analyses indicate that D. oleifera is closely related to Diospyros kaki Thunb. and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and elucidate the molecular mechanisms of important traits. Findings The D. oleifera genome was assembled with 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was ∼812.3 Mb and had a high level of continuity with N50 of 3.36 Mb. Fifteen scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. Repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes were expanded in the D. oleifera genome compared with Diospyros lotus, Camellia sinensis, and Vitis vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient γ event, a second whole-genome duplication event occurred in D. oleifera and D. lotus. Conclusions We generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros.

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