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Ren Y, Dong W, Chen J, Xue H, Bu W. Identification and function of microRNAs in hemipteran pests: A review. INSECT SCIENCE 2024. [PMID: 39292965 DOI: 10.1111/1744-7917.13449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/20/2024]
Abstract
Hemiptera is one of the most significant orders of insect pests, including whiteflies, true bugs, aphids, planthoppers, psyllids, and so forth, which have led to substantial economic losses in agricultural industries and have significantly affected food yields through their ability to suck the phloem sap of crops and transmit numerous bacterial and viral pathogens. Therefore, explorations of pest-specific, eco-friendly and easy-to-adopt technologies for hemipteran pest control are urgently needed. To the best of our knowledge, microRNAs (miRNAs), which are endogenous non-coding small RNAs approximately 22 nucleotides in length, are involved in regulating gene expression via the direct recognition and binding of the 3'-untranslated region (3'-UTR) of target messenger RNAs (mRNAs) or by acting as a center of a competitive endogenous RNA (ceRNA) network at the post-transcriptional level. This review systematically outlines the characterization and functional investigation of the miRNA biogenesis pathway in hemipteran pests, such as whiteflies, true bugs, aphids and planthoppers. In addition, we explored the results of small RNA sequencing and functional observations of miRNAs in these pests, and the results suggest that the numerous miRNAs obtained and annotated via high-throughput sequencing technology and bioinformatic analyses contribute to molting development, fitness, wing polyphenism, symbiont interactions and insecticide resistance in hemipteran pests. Finally, we summarize current advances and propose a framework for future research to extend the current data and address potential limitations in the investigation and application of hemipteran miRNAs.
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Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenhao Dong
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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2
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Prajapati MR, Kumar P, Pratap Singh R, Shanker R, Singh J, Kumar Bharti M, Singh R, Verma H, Gangwar LK, Singh Gaurav S, Kapoor N, Prakash S, Dixit R. De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm. J Genet Eng Biotechnol 2024; 22:100393. [PMID: 39179316 PMCID: PMC11179078 DOI: 10.1016/j.jgeb.2024.100393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/08/2024] [Accepted: 05/20/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND The cabbage webworm, Hellula undalis (Fabricius) (Lepidoptera: Pyralidae), is a significant pest of brassicas and other cruciferous plants in warm regions worldwide. Transcriptome analysis is valuable for investigation of molecular mechanisms underlying the insect development and reproduction. De novo assembly is particularly useful for acquiring complete transcriptome information of insect species when there is no reference genome available. In case of Hellula undalis, only 17 nucleotide records are currently available throughout NCBI nucleotide database. Genes associated with metabolic processes, general development, reproduction, defense and functional genomics were not previously predicted in the Hellula undalis at the genomic level. METHODS & RESULTS To address this issue, we constructed Hellula undalis transcriptome using Illumina NovaSeq6000 technology. Approximately 48 million 150 bp paired-end reads were obtained from sequencing. A total of 30,451 contigs were generated by de novo assembly of sample and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 71 % of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 123 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we compared the ortholog gene family of the Hullula undalis, transcriptome to Spodoptera frugiperda, spodotera litura and spodoptera littoralis and found that 391 orthologous gene families are specific to Hullula undalis. A total of 1,913 potential SSRs was discovered in Hullula undalis contigs. CONCLUSIONS This study is the first transcriptome data for Hullula undalis. Additionally, it serves as a valuable resource for identifying target genes and developing effective and environmentally friendly strategies for pest control.
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Affiliation(s)
- Malyaj R Prajapati
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Pankaj Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India.
| | - Reetesh Pratap Singh
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Ravi Shanker
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Jitender Singh
- Chaudhary Charan Singh University, Meerut, Uttar Pradesh 250001, India.
| | - Mahesh Kumar Bharti
- College of Veterinary and Animal Sciences, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Rajendra Singh
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Harshit Verma
- College of Veterinary and Animal Sciences, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - L K Gangwar
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | | | - Neelesh Kapoor
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Satya Prakash
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
| | - Rekha Dixit
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh 250110, India
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3
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Just J, Laslo M, Lee YJ, Yarnell M, Zhang Z, Angelini DR. Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bug Oncopeltus fasciatus. Proc Biol Sci 2023; 290:20222083. [PMID: 36722087 PMCID: PMC9890105 DOI: 10.1098/rspb.2022.2083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
Sexual dimorphism is common in animals. The most complete model of sex determination comes from Drosophila melanogaster, where the relative dosage of autosomes and X chromosomes leads indirectly to sex-specific transcripts of doublesex (dsx). Female Dsx interacts with a mediator complex protein encoded by intersex (ix) to activate female development. In males, the transcription factor encoded by fruitless (fru) promotes male-specific behaviour. The genetics of sex determination have been examined in a small number of other insects, yet several questions remain about the plesiomorphic state. Is dsx required for female and male development? Is fru conserved in male behaviour or morphology? Are other components such as ix functionally conserved? To address these questions, we report expression and functional tests of dsx, ix and fru in the hemipteran Oncopeltus fasciatus, characterizing three sexual dimorphisms. dsx prevents ix phenotypes in all sexes and dimorphic traits in the milkweed bug. ix and fru are expressed across the body, in females and males. fru and ix also affect the genitalia of both sexes, but have effects limited to different dimorphic structures in different sexes. These results reveal roles for ix and fru distinct from other insects, and demonstrate distinct development mechanisms in different sexually dimorphic structures.
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Affiliation(s)
- Josefine Just
- Department of Biology, Colby College, 5700 Mayflower Hill, Waterville, ME 04901, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Mara Laslo
- Curriculum Fellows Program, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Ye Jin Lee
- Department of Biology, Colby College, 5700 Mayflower Hill, Waterville, ME 04901, USA
| | - Michael Yarnell
- Department of Pediatrics, University of Colorado School of Medicine, 13123 East 16th Avenue, B065, Aurora, CO 80045, USA
| | - Zhuofan Zhang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, 777 Atlantic Drive, Atlanta, GA 30332, USA
| | - David R. Angelini
- Department of Biology, Colby College, 5700 Mayflower Hill, Waterville, ME 04901, USA
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4
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Dynamics of maternal gene expression in Rhodnius prolixus. Sci Rep 2022; 12:6538. [PMID: 35449214 PMCID: PMC9023505 DOI: 10.1038/s41598-022-09874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
The study of developmental processes in Rhodnius prolixus has recently advanced with the sequencing of the genome. In this work, we analyze the maternal gene expression driving oogenesis and early embryogenesis in R. prolixus. We examined the transcriptional profile of mRNAs to establish the genes expressed across the ovary, unfertilized eggs and different embryonic stages of R. prolixus until the formation of the germ band anlage (0, 12, 24, and 48 h post egg laying). We identified 81 putative maternal and ovary-related genes and validated their expression by qRT-PCR. We validate the function of the ortholog gene Bicaudal-D (Rp-BicD) by in situ hybridization and parental RNAi. Consistent with a role in oogenesis and early development of R. prolixus, we show that lack of Rp-BicD does not significantly affect oogenesis but impairs the formation of the blastoderm. Based on our findings, we propose three times of action for maternal genes during oogenesis and embryogenesis in R. prolixus.
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5
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Wilson RJ, Ahmed TH, Rahman MM, Cartwright BM, Jones TC. Identification and activity of monoamine oxidase in the orb-weaving spider Larinioides cornutus. Gen Comp Endocrinol 2020; 299:113580. [PMID: 32827514 DOI: 10.1016/j.ygcen.2020.113580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022]
Abstract
Monoamine oxidase (MAO) is a mitochondrial membrane-bound enzyme that catalyzes the oxidative deamination of monoamines in a wide array of organisms. While the enzyme monoamine oxidase has been studied extensively in its role in moderating behavior in mammals, there is a paucity of research investigating this role in invertebrates, where the latter utilizes this enzyme in a major pathway to degrade monoamines. There is especially a dismal lack of information on how MAO influences activity in invertebrates, particularly in account of the circadian cycle. Previous studies revealed MAO degrades serotonin and norepinephrine in arachnids, but did not investigate other critically important compounds like octopamine. Larinioides cornutus is a species of orb-weaving spider that exhibits diel fluctuations in behavior, specifically levels of aggression. The monoamines octopamine and serotonin have been shown to influence aggressive behaviors in L. cornutus, thus this species was used to investigate if MAO is a potential site of regulation throughout the day. Not only did gene expression of MAO orthologs and MAO activity fluctuate at different times of day, but the enzymatic activity was substrate-specific producing a higher level of degradation of octopamine as compared to serotonin in vitro. This study further supports evidence that MAO has an active role in monoamine inactivation in invertebrates and provides a first look at how MAO ultimately may be regulating behavior in an invertebrate.
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Affiliation(s)
- Rebecca J Wilson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37601, United States.
| | - Tahmina H Ahmed
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Md Mahbubur Rahman
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Brian M Cartwright
- Department of Biomedical Sciences, Quillen College of Medicine, Johnson City, TN 37601, United States
| | - Thomas C Jones
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37601, United States
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6
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Benton MA, Frey N, Nunes da Fonseca R, von Levetzow C, Stappert D, Hakeemi MS, Conrads KH, Pechmann M, Panfilio KA, Lynch JA, Roth S. Fog signaling has diverse roles in epithelial morphogenesis in insects. eLife 2019; 8:47346. [PMID: 31573513 PMCID: PMC6794076 DOI: 10.7554/elife.47346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The Drosophila Fog pathway represents one of the best-understood signaling cascades controlling epithelial morphogenesis. During gastrulation, Fog induces apical cell constrictions that drive the invagination of mesoderm and posterior gut primordia. The cellular mechanisms underlying primordia internalization vary greatly among insects and recent work has suggested that Fog signaling is specific to the fast mode of gastrulation found in some flies. On the contrary, here we show in the beetle Tribolium, whose development is broadly representative for insects, that Fog has multiple morphogenetic functions. It modulates mesoderm internalization and controls a massive posterior infolding involved in gut and extraembryonic development. In addition, Fog signaling affects blastoderm cellularization, primordial germ cell positioning, and cuboidal-to-squamous cell shape transitions in the extraembryonic serosa. Comparative analyses with two other distantly related insect species reveals that Fog's role during cellularization is widely conserved and therefore might represent the ancestral function of the pathway.
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Affiliation(s)
- Matthew Alan Benton
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Nadine Frey
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | | | - Cornelia von Levetzow
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Dominik Stappert
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Muhammad Salim Hakeemi
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Kai H Conrads
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Matthias Pechmann
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Kristen A Panfilio
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois, Chicago, United States
| | - Siegfried Roth
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
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7
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Reding K, Chen M, Lu Y, Cheatle Jarvela AM, Pick L. Shifting roles of Drosophila pair-rule gene orthologs: segmental expression and function in the milkweed bug Oncopeltus fasciatus. Development 2019; 146:dev181453. [PMID: 31444220 PMCID: PMC6765130 DOI: 10.1242/dev.181453] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023]
Abstract
The discovery of pair-rule genes (PRGs) in Drosophila revealed the existence of an underlying two-segment-wide prepattern directing embryogenesis. The milkweed bug Oncopeltus fasciatus, a hemimetabolous insect, is a more representative arthropod: most of its segments form sequentially after gastrulation. Here, we report the expression and function of orthologs of the complete set of nine Drosophila PRGs in Oncopeltus Seven Of-PRG-orthologs are expressed in stripes in the primordia of every segment, rather than every other segment; Of-runt is PR-like and several orthologs are also expressed in the segment addition zone. RNAi-mediated knockdown of Of-odd-skipped, paired and sloppy-paired impacted all segments, with no indication of PR-like register. We confirm that Of-E75A is expressed in PR-like stripes, although it is not expressed in this way in Drosophila, demonstrating the existence of an underlying PR-like prepattern in Oncopeltus These findings reveal that a switch occurred in regulatory circuits, leading to segment formation: while several holometabolous insects are 'Drosophila-like', using PRG orthologs for PR patterning, most Of-PRGs are expressed segmentally in Oncopeltus, a more basally branching insect. Thus, an evolutionarily stable phenotype - segment formation - is directed by alternate regulatory pathways in diverse species.
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Affiliation(s)
- Katie Reding
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD 20742, USA
| | - Mengyao Chen
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD 20742, USA
| | - Yong Lu
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD 20742, USA
| | - Alys M Cheatle Jarvela
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD 20742, USA
| | - Leslie Pick
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD 20742, USA
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8
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Hoang NV, Furtado A, Perlo V, Botha FC, Henry RJ. The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome. Front Genet 2019; 10:654. [PMID: 31396260 PMCID: PMC6664245 DOI: 10.3389/fgene.2019.00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.
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Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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9
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019. [PMID: 30935422 DOI: 10.1101/201731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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10
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019; 20:64. [PMID: 30935422 PMCID: PMC6444547 DOI: 10.1186/s13059-019-1660-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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11
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Comparative transcriptome analysis explores maternal to zygotic transition during Eriocheir sinensis early embryogenesis. Gene 2019; 685:12-20. [PMID: 30321661 DOI: 10.1016/j.gene.2018.10.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 11/21/2022]
Abstract
The maternal genome directs almost all aspects of early animal development. As development proceeds, the elimination of maternal gene products and zygotic genome activation (ZGA) occur during the maternal to zygotic transition (MZT). To study the molecular mechanisms regulating this developmental event in Eriocheir sinensis, RNA-Seq technology was applied to generate comprehensive information on transcriptome dynamics during early embryonic stages. In total, 32,088 annotated unigenes were obtained from the transcriptomes of fertilized eggs and embryos at the cleavage (2-4 cell) and blastula stage. A total of 566 maternal genes and 1165 zygotic genes were isolated, among which 103 and 266 genes were predicted conserved maternal transcripts (COMATs) and conserved zygotic transcripts (COZYTs), respectively. The COMATs performed housekeeping gene functions and may be essential for initiating early embryogenesis of the Bilateria. Furthermore, 87, 76 and 117 differentially expressed genes associated with the MZT, morphogenesis and immunity were identified when compared the three transcriptomic datasets. We also unmask that the MZT takes place around the cleavage stage, when the genes involved in the clearance of maternal gene products and the ZGA were significantly up-regulated. Taken together, these datasets provide a valuable resource for understanding the mechanisms of early developmental events in E. sinensis, and facilitate further studies on molecular mechanisms of asynchronous development in crabs.
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12
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Santibáñez-López CE, Ontano AZ, Harvey MS, Sharma PP. Transcriptomic Analysis of Pseudoscorpion Venom Reveals a Unique Cocktail Dominated by Enzymes and Protease Inhibitors. Toxins (Basel) 2018; 10:E207. [PMID: 29783636 PMCID: PMC5983263 DOI: 10.3390/toxins10050207] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/19/2022] Open
Abstract
Transcriptomic and genomic analyses have illuminated the diversity of venoms in three of the four venomous arachnid orders (scorpions, spiders, and ticks). To date, no venom gland transcriptome analysis has been available for pseudoscorpions, the fourth venomous arachnid lineage. To redress this gap, we sequenced an mRNA library generated from the venom glands of the species Synsphyronus apimelus (Garypidae). High-throughput sequencing by the Illumina protocol, followed by de novo assembly, resulted in a total of 238,331 transcripts. From those, we annotated 131 transcripts, which code for putative peptides/proteins with similar sequences to previously reported venom components available from different arachnid species in protein databases. Transcripts putatively coding for enzymes showed the richest diversity, followed by other venom components such as peptidase inhibitors, cysteine-rich peptides, and thyroglobulin 1-like peptides. Only 11 transcripts were found that code for putatively low molecular mass spider toxins. This study constitutes the first report of the diversity of components within pseudoscorpion venom.
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Affiliation(s)
- Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA.
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, Ciudad de México C.P. 04510, Mexico.
| | - Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA.
| | - Mark S Harvey
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia.
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA.
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13
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Xavier MA, Tirloni L, Pinto AFM, Diedrich JK, Yates JR, Mulenga A, Logullo C, da Silva Vaz I, Seixas A, Termignoni C. A proteomic insight into vitellogenesis during tick ovary maturation. Sci Rep 2018; 8:4698. [PMID: 29549327 PMCID: PMC5856802 DOI: 10.1038/s41598-018-23090-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/06/2018] [Indexed: 01/22/2023] Open
Abstract
Ticks are arthropod ectoparasites of importance for public and veterinary health. The understanding of tick oogenesis and embryogenesis could contribute to the development of novel control methods. However, to date, studies on the temporal dynamics of proteins during ovary development were not reported. In the present study we followed protein profile during ovary maturation. Proteomic analysis of ovary extracts was performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using shotgun strategy, in addition to dimethyl labelling-based protein quantification. A total of 3,756 proteins were identified, which were functionally annotated into 30 categories. Circa 80% of the annotated proteins belong to categories related to basal metabolism, such as protein synthesis and modification machineries, nuclear regulation, cytoskeleton, proteasome machinery, transcriptional machinery, energetic metabolism, extracellular matrix/cell adhesion, immunity, oxidation/detoxification metabolism, signal transduction, and storage. The abundance of selected proteins involved in yolk uptake and degradation, as well as vitellin accumulation during ovary maturation, was assessed using dimethyl-labelling quantification. In conclusion, proteins identified in this study provide a framework for future studies to elucidate tick development and validate candidate targets for novel control methods.
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Affiliation(s)
- Marina Amaral Xavier
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lucas Tirloni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Antônio F M Pinto
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Albert Mulenga
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Carlos Logullo
- Laboratório de Sanidade Animal, Laboratório de Química e Função de Proteínas e Peptídeos and Unidade de Experimentação Animal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Adriana Seixas
- Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Carlos Termignoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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14
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Transcriptome Analysis of the Biosynthesis of Anthocyanins in Begonia semperflorens under Low-Temperature and High-Light Conditions. FORESTS 2018. [DOI: 10.3390/f9020087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Panfilio KA, Angelini DR. By land, air, and sea: hemipteran diversity through the genomic lens. CURRENT OPINION IN INSECT SCIENCE 2018; 25:106-115. [PMID: 29602356 DOI: 10.1016/j.cois.2017.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Thanks to a recent spate of sequencing projects, the Hemiptera are the first hemimetabolous insect order to achieve a critical mass of species with sequenced genomes, establishing the basis for comparative genomics of the bugs. However, as the most speciose hemimetabolous order, there is still a vast swathe of the hemipteran phylogeny that awaits genomic representation across subterranean, terrestrial, and aquatic habitats, and with lineage-specific and developmentally plastic cases of both wing polyphenisms and flightlessness. In this review, we highlight opportunities for taxonomic sampling beyond obvious pest species candidates, motivated by intriguing biological features of certain groups as well as the rich research tradition of ecological, physiological, developmental, and particularly cytogenetic investigation that spans the diversity of the Hemiptera.
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Affiliation(s)
- Kristen A Panfilio
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom; Institute of Zoology: Developmental Biology, University of Cologne, 50674 Cologne, Germany.
| | - David R Angelini
- Department of Biology, Colby College, Waterville, ME 04901, United States
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16
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Gu J, Dai S, Liu H, Cao Q, Yin S, Lai KP, Tse WKF, Wong CKC, Shi H. Identification of immune-related genes in gill cells of Japanese eels (Anguilla japonica) in adaptation to water salinity changes. FISH & SHELLFISH IMMUNOLOGY 2018; 73:288-296. [PMID: 29269288 DOI: 10.1016/j.fsi.2017.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
The changes in ambient salinity influence ion and water homeostasis, hormones secretion, and immune response in fish gills. The physiological functions of hormones and ion transporters in the regulation of gill-osmoregulation have been widely studied, however the modulation of immune response under salinity changes is not determined. Using transcriptome sequencing, we obtained a comprehensive profile of osmo-responsive genes in gill cells of Japanese eel (Anguilla japonica). Herein, we applied bioinformatics analysis to identify the immune-related genes that were significantly higher expressed in gill pavement cells (PVCs) and mitochondrial-rich cells (MRCs) in freshwater (FW) than seawater (SW) adapted fish. We validated the data using the real-time qPCR, which showed a high correlation between the RNA-seq and real-time qPCR data. In addition, the immunohistochemistry results confirmed the changes of the expression of selected immune-related genes, including C-reactive protein (CRP) in PVCs, toll-like receptor 2 (TLR2) in MRCs and interleukin-1 receptor type 2 (IL-1R2) in both PVCs and MRCs. Collectively our results demonstrated that those immune-related genes respond to salinity changes, and might trigger related special signaling pathways and network. This study provides new insights into the impacts of ambient salinity changes on adaptive immune response in fish gill cells.
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Affiliation(s)
- Jie Gu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Shuya Dai
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Haitao Liu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Quanquan Cao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Keng Po Lai
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | | | | | - Haifeng Shi
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China.
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17
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Zhao JS, Wang AY, Zhao HB, Chen YH. Transcriptome sequencing and differential gene expression analysis of the schistosome-transmitting snail Oncomelania hupensis inhabiting hilly and marshland regions. Sci Rep 2017; 7:15809. [PMID: 29150650 PMCID: PMC5693929 DOI: 10.1038/s41598-017-16084-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/07/2017] [Indexed: 12/18/2022] Open
Abstract
The freshwater snail Oncomelania hupensis is the unique intermediate host of the blood fluke Schistosoma japonicum, which is the major cause of schistosomiasis. The snail inhabits two contrasting environments: the hilly and marshland regions. The hilly snails are smaller in size and have the typical smooth shell, whereas the marshland snails are larger and possess the ribbed shell. To reveal the differences in gene expression between the hilly and marshland snails, a total of six snails, three per environment, were individually examined by RNA sequencing technology. All paired-end reads were assembled into contigs from which 34,760 unigenes were predicted. Based on single nucleotide polymorphisms, principal component analysis and neighbor-joining clustering revealed two distinct clusters of hilly and marshland snails. Analysis of expression changes between environments showed that upregulated genes relating to immunity and development were enriched in hilly snails, while those associated with reproduction were over-represented in marshland snails. Eight differentially expressed genes between the two types of snails were validated by qRT-PCR. Our study identified candidate genes that could be targets for future functional studies, and provided a link between expression profiling and ecological adaptation of the snail that may have implications for schistosomiasis control.
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Affiliation(s)
- Jin-Song Zhao
- School of Basic Medicine, Wannan Medical College, Wuhu, 241002, China
| | - An-Yun Wang
- School of Public Health, Wannan Medical College, Wuhu, 241002, China
| | - Hua-Bin Zhao
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan-Hong Chen
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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18
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Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R. Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans. Sci Rep 2017; 7:13547. [PMID: 29051502 PMCID: PMC5648782 DOI: 10.1038/s41598-017-13176-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeng 4, 6708 WE, Wageningen, The Netherlands
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- Biological Sciences Department, NYC College of Technology, City University of New York, 300 Jay Street, Brooklyn, New York, 11201, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Heike Hadrys
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- ITZ, Ecology&Evolution, University of Veterinary Medicine Hanover, Buenteweg 17d, D-30559, Hannover, Germany
- Yale University, Department of Ecology & Evolutionary Biology, 165 Prospect Street, New Haven, CT, 06511, USA
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
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19
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Temporal transcriptomic profiling of the ant-feeding assassin bug Acanthaspis cincticrus reveals a biased expression of genes associated with predation in nymphs. Sci Rep 2017; 7:12691. [PMID: 28978945 PMCID: PMC5627237 DOI: 10.1038/s41598-017-12978-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Acanthaspis cincticrus (Stål) is an assassin bug with a specialized camouflaging behavior to ambush ants in the nymphal stages. In this study, we comprehensively sequenced all the life stages of A. cincticrus, including the eggs, five nymph instars, female and male adults using Illumina HiSeq technology. We obtained 176 million clean sequence reads. The assembled 84,055 unigenes were annotated and classified functionally based on protein databases. Among the unigenes, 29.03% were annotated by one or more databases, suggesting their well-conserved functions. Comparison of the gene expression profiles in the egg, nymph and adult stages revealed certain bias. Functional enrichment analysis of significantly differentially expressed genes (SDEGs) showed positive correlation with specific physiological processes within each stage, including venom, aggression, olfactory recognition as well as growth and development. Relative expression of ten SDEGs involved in predation process was validated using quantitative real-time PCR (qRT-PCR).
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20
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Chipman AD. Oncopeltus fasciatus
as an evo-devo research organism. Genesis 2017; 55. [DOI: 10.1002/dvg.23020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/29/2016] [Accepted: 01/15/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ariel D. Chipman
- The Department of Ecology; Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus; Givat Ram Jerusalem 91904 Israel
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21
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Nunes-da-Fonseca R, Berni M, Tobias-Santos V, Pane A, Araujo HM. Rhodnius prolixus: From classical physiology to modern developmental biology. Genesis 2017; 55. [DOI: 10.1002/dvg.22995] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Rodrigo Nunes-da-Fonseca
- Laboratório Integrado de Ciências Morfofuncionais; Núcleo em Ecologia e Desenvolvimento Socio-Ambiental de Macaé, Campus Macaé, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- Laboratório de Biologia Molecular do Desenvolvimento Instituto de Ciências Biomédicas, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Mateus Berni
- Institute of Molecular Entomology; INCT-EM
- Laboratório de Biologia Molecular do Desenvolvimento Instituto de Ciências Biomédicas, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Vitória Tobias-Santos
- Laboratório Integrado de Ciências Morfofuncionais; Núcleo em Ecologia e Desenvolvimento Socio-Ambiental de Macaé, Campus Macaé, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
- Institute of Molecular Entomology; INCT-EM
| | - Attilio Pane
- Institute of Molecular Entomology; INCT-EM
- Laboratório de Biologia Molecular do Desenvolvimento Instituto de Ciências Biomédicas, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Helena Marcolla Araujo
- Institute of Molecular Entomology; INCT-EM
- Laboratório de Biologia Molecular do Desenvolvimento Instituto de Ciências Biomédicas, Federal University of Rio de Janeiro; Rio de Janeiro Brazil
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22
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Carlson DE, Hedin M. Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PLoS One 2017; 12:e0174102. [PMID: 28379977 PMCID: PMC5381867 DOI: 10.1371/journal.pone.0174102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/04/2017] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.
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Affiliation(s)
- David E. Carlson
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, United States of America
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23
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Irles P, Ramos S, Piulachs MD. SPARC preserves follicular epithelium integrity in insect ovaries. Dev Biol 2017; 422:105-114. [DOI: 10.1016/j.ydbio.2017.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 02/06/2023]
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24
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Transcriptome Characterization of Dendrolimus punctatus and Expression Profiles at Different Developmental Stages. PLoS One 2016; 11:e0161667. [PMID: 27560151 PMCID: PMC4999207 DOI: 10.1371/journal.pone.0161667] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/09/2016] [Indexed: 11/19/2022] Open
Abstract
The pine moth Dendrolimus punctatus (Walker) is a common insect pest that confers serious damage to conifer forests in south of China. Extensive physiology and ecology studies on D. punctatus have been carried out, but the lack of genetic information has limited our understanding of the molecular mechanisms behind its development and resistance. Using RNA-seq approach, we characterized the transcriptome of this pine moth and investigated its developmental expression profiles during egg, larval, pupal, and adult stages. A total of 107.6 million raw reads were generated that were assembled into 70,664 unigenes. More than 30% unigenes were annotated by searching for homology in protein databases. To better understand the process of metamorphosis, we pairwise compared four developmental phases and obtained 17,624 differential expression genes. Functional enrichment analysis of differentially expressed genes showed positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study provides a valuable genomic resource of D. punctatus covering all its developmental stages, and will promote future studies on biological processes at the molecular level.
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25
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Lai KP, Li JW, Chan CYS, Chan TF, Yuen KWY, Chiu JMY. Transcriptomic alterations in Daphnia magna embryos from mothers exposed to hypoxia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 177:454-463. [PMID: 27399157 DOI: 10.1016/j.aquatox.2016.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Hypoxia occurs when dissolved oxygen (DO) falls below 2.8mgL(-1) in aquatic environments. It can cause trans-generational effects not only in fish, but also in the water fleas Daphnia. In this study, transcriptome sequencing analysis was employed to identify transcriptomic alterations induced by hypoxia in embryos of Daphnia magna, with an aim to investigate the mechanism underlying the trans-generational effects caused by hypoxia in Daphnia. The embryos (F1) were collected from adults (F0) that were previously exposed to hypoxia (or normoxia) for their whole life. De novo transcriptome assembly identified 18270 transcripts that were matched to the UniProtKB/Swiss-Prot database and resulted in 7419 genes. Comparative transcriptome analysis showed 124 differentially expressed genes, including 70 up- and 54 down-regulated genes under hypoxia. Gene ontology analysis further highlighted three clusters of genes which revealed acclimatory changes of haemoglobin, suppression in vitellogenin gene family and histone modifications. Specifically, the expressions of histone H2B, H3, H4 and histone deacetylase 4 (HDAC4) were deregulated. This study suggested that trans-generational effects of hypoxia on Daphnia may be mediated through epigenetic regulations of histone modifications.
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Affiliation(s)
- Keng-Po Lai
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong
| | - Jing-Woei Li
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | | | - Ting-Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
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26
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Ješovnik A, González VL, Schultz TR. Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma. PLoS One 2016; 11:e0151059. [PMID: 27466804 PMCID: PMC4965065 DOI: 10.1371/journal.pone.0151059] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/22/2016] [Indexed: 01/27/2023] Open
Abstract
Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus Sericomyrmex and a single lower-attine ant species, Apterostigma megacephala, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee Apis mellifera for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6-66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus Sericomyrmex. This result is further confirmed by a separate analysis of the three Sericomyrmex species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly argininosuccinate synthase and argininosuccinate lyase, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for Sericomyrmex species, the absence of arginine anabolic genes in the lower-attine ant Apterostigma megacephala strongly suggests that the loss coincided with the origin of attine ants.
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Affiliation(s)
- Ana Ješovnik
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
- Maryland Center for Systematic Entomology, Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Vanessa L. González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Ted R. Schultz
- Entomology Department, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
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Qi L, Fang Q, Zhao L, Xia H, Zhou Y, Xiao J, Li K, Ye G. De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae. PLoS One 2016; 11:e0159258. [PMID: 27428371 PMCID: PMC4948883 DOI: 10.1371/journal.pone.0159258] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/29/2016] [Indexed: 12/15/2022] Open
Abstract
The small white butterfly Pieris rapae is one of the most destructive pests of Brassicaceae. Yet little is understood about its genes involved in development. To facilitate research on P. rapae, we sequenced the transcriptome of P. rapae during six developmental stages, including the egg, three larval stages, the pupa, and the adult. In total, 240 million high-quality reads were obtained. De novo assembly generated 96,069 unigenes with an average length of 1353 nt. Of these, 31,629 unigenes had homologs as determined by a blastx search against the NR database with a cut-off e-value of 10−5. Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to functionally annotate those genes. Then, 849 genes involved in seven canonical development signaling pathway were identified, including dozens of key genes such as Hippo, Notch, and JAK2. A total of 21,883 differentially expressed (cut-off of 2-fold) unigenes were detected across the developmental stages, most of which were found between the egg and first larval stages. Interestingly, only 34 differentially expressed unigenes, most of which are cuticle protein related genes, were detected with a cut-off of 210-fold. Furthermore, we identified 32 heat shock protein (Hsp) genes that were expressed with complete open reading frames. Based on phylogenetic trees of the Hsp genes, we found that Hsp genes with close evolutionary relationships had similar expression pattern. Additionally, partial pattern recognition receptors genes were found to be developmental regulated. This study provides comprehensive sequence resources for P. rapae and numerous differential expressed genes, and these findings will lay the foundation for future functional genomics studies on this species.
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Affiliation(s)
- Lixing Qi
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Qi Fang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Lei Zhao
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Hao Xia
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Yuxun Zhou
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Junhua Xiao
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Kai Li
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Horn RL, Ramaraj T, Devitt NP, Schilkey FD, Cowley DE. De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. Mol Ecol Resour 2016; 17:161-171. [PMID: 27292122 DOI: 10.1111/1755-0998.12555] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/05/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023]
Abstract
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
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Affiliation(s)
- Rebekah L Horn
- Biology Department, Trent University, 1600 West Bank Drive, Peterborough, ON, Canada, K9J 7B8
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Faye D Schilkey
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - David E Cowley
- Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Box 30003, MSC 4901, Las Cruces, NM, 88003, USA
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Toubiana W, Khila A. The benefits of expanding studies of trait exaggeration to hemimetabolous insects and beyond morphology. Curr Opin Genet Dev 2016; 39:14-20. [PMID: 27318690 DOI: 10.1016/j.gde.2016.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 12/01/2022]
Abstract
Trait exaggeration, well known to naturalists and evolutionary biologists, has recently become a prominent research subject in the modern field of Evolutionary Developmental Biology. A large number of traits that can be considered as cases of exaggeration exist in nature. Yet, the field has almost exclusively focused on the study of growth-related exaggerated traits in a selection of holometabolous insects. The absence of the hemimetabola from studies of exaggeration leaves a significant gap in our understanding of the development and evolution of such traits. Here we argue that efforts to understand the mechanisms of trait exaggeration would benefit from expanding the study subjects to include other kinds of exaggeration and other model species.
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Affiliation(s)
- William Toubiana
- Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - Université Claude Bernard Lyon-1, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - Université Claude Bernard Lyon-1, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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Jiang H, Li X, Sun Y, Hou F, Zhang Y, Li F, Gu Z, Liu X. Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis. PLoS One 2016; 11:e0157173. [PMID: 27280288 PMCID: PMC4900531 DOI: 10.1371/journal.pone.0157173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/25/2016] [Indexed: 11/27/2022] Open
Abstract
Background The oriental river prawn (Macrobrachium nipponense) is the most prevalent aquaculture species in China. The sexual precocity in this species has received considerable attention in recent years because more and more individuals matured at a small size, which devalues the commercial production. In this study, we developed deep-coverage transcriptomic sequencing data for the ovaries of sexually precocious and normal sexually mature M. nipponense using next-generation RNA sequencing technology and attempted to provide the first insight into the molecular regulatory mechanism of sexual precocity in this species. Results A total of 63,336 unigenes were produced from the ovarian cDNA libraries of sexually precocious and normal sexually mature M. nipponense using Illumina HiSeq 2500 platform. Through BLASTX searches against the NR, STRING, Pfam, Swissprot and KEGG databases, 15,134 unigenes were annotated, accounting for 23.89% of the total unigenes. 5,195 and 3,227 matched unigenes were categorized by GO and COG analysis respectively. 15,908 unigenes were consequently mapped into 332 KEGG pathways, and many reproduction-related pathways and genes were identified. Moreover, 26,008 SSRs were identified from 18,133 unigenes. 80,529 and 80,516 SNPs were yielded from ovarian libraries of sexually precocious and normal sexually mature prawn, respectively, and 29,851 potential SNPs between these two groups were also predicted. After comparing the ovarian libraries of sexually precocious and normal sexually mature prawn, 549 differentially expressed genes (DEGs) and 9 key DEGs that may be related to sexual precocity of M. nipponense were identified. 20 DEGs were selected for validation by quantitative real-time PCR (QPCR) and 19 DEGs show consistent expression between QPCR and RNAseq-based differential expression analysis datasets. Conclusion This is the first report on the large-scale RNA sequencing of ovaries of sexually precocious and normal sexually mature M. nipponense. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of M. nipponense. The large number of candidate SNPs and SSRs detected in this study could be used as genetic markers for population genetics and functional genomics in this species. More importantly, many DEGs, especially nine key DEGs between sexually precocious and normal sexually mature prawns were identified, which will dramatically improve understanding of molecular regulatory mechanism of sexual precocity of this species.
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Affiliation(s)
- Hongxia Jiang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People’s Republic of China
- College of Fisheries, Henan Normal University, Xinxiang, Henan, People’s Republic of China
| | - Xilian Li
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People’s Republic of China
| | - Yuhang Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
| | - Fujun Hou
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
| | - Yufei Zhang
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People’s Republic of China
| | - Fei Li
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People’s Republic of China
| | - Zhimin Gu
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, People’s Republic of China
- * E-mail: (ZG); (XL)
| | - Xiaolin Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
- * E-mail: (ZG); (XL)
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Insilco Prediction and Characterization of microRNAs from Oncopeltus fasciatus (Hemiptera: Lygaeidae) Genome. Appl Biochem Biotechnol 2016; 179:1393-403. [DOI: 10.1007/s12010-016-2072-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
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Esquivel CJ, Cassone BJ, Piermarini PM. A de novo transcriptome of the Malpighian tubules in non-blood-fed and blood-fed Asian tiger mosquitoes Aedes albopictus: insights into diuresis, detoxification, and blood meal processing. PeerJ 2016; 4:e1784. [PMID: 26989622 PMCID: PMC4793337 DOI: 10.7717/peerj.1784] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/19/2016] [Indexed: 01/17/2023] Open
Abstract
Background. In adult female mosquitoes, the renal (Malpighian) tubules play an important role in the post-prandial diuresis, which removes excess ions and water from the hemolymph of mosquitoes following a blood meal. After the post-prandial diuresis, the roles that Malpighian tubules play in the processing of blood meals are not well described. Methods. We used a combination of next-generation sequencing (paired-end RNA sequencing) and physiological/biochemical assays in adult female Asian tiger mosquitoes (Aedes albopictus) to generate molecular and functional insights into the Malpighian tubules and how they may contribute to blood meal processing (3–24 h after blood ingestion). Results/Discussion. Using RNA sequencing, we sequenced and assembled the first de novo transcriptome of Malpighian tubules from non-blood-fed (NBF) and blood-fed (BF) mosquitoes. We identified a total of 8,232 non-redundant transcripts. The Malpighian tubules of NBF mosquitoes were characterized by the expression of transcripts associated with active transepithelial fluid secretion/diuresis (e.g., ion transporters, water channels, V-type H+-ATPase subunits), xenobiotic detoxification (e.g., cytochrome P450 monoxygenases, glutathione S-transferases, ATP-binding cassette transporters), and purine metabolism (e.g., xanthine dehydrogenase). We also detected the expression of transcripts encoding sodium calcium exchangers, G protein coupled-receptors, and septate junctional proteins not previously described in mosquito Malpighian tubules. Within 24 h after a blood meal, transcripts associated with active transepithelial fluid secretion/diuresis exhibited a general downregulation, whereas those associated with xenobiotic detoxification and purine catabolism exhibited a general upregulation, suggesting a reinvestment of the Malpighian tubules’ molecular resources from diuresis to detoxification. Physiological and biochemical assays were conducted in mosquitoes and isolated Malpighian tubules, respectively, to confirm that the transcriptomic changes were associated with functional consequences. In particular, in vivo diuresis assays demonstrated that adult female mosquitoes have a reduced diuretic capacity within 24 h after a blood meal. Moreover, biochemical assays in isolated Malpighian tubules showed an increase in glutathione S-transferase activity and the accumulation of uric acid (an end product of purine catabolism) within 24 h after a blood meal. Our data provide new insights into the molecular physiology of Malpighian tubules in culicine mosquitoes and reveal potentially important molecular targets for the development of chemical and/or gene-silencing insecticides that would disrupt renal function in mosquitoes.
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Affiliation(s)
- Carlos J Esquivel
- Department of Entomology, The Ohio State University/Ohio Agricultural Research and Development Center , Wooster, OH , United States
| | - Bryan J Cassone
- Department of Biology, Brandon University , Brandon, Manitoba , Canada
| | - Peter M Piermarini
- Department of Entomology, The Ohio State University/Ohio Agricultural Research and Development Center , Wooster, OH , United States
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Pérez-Portela R, Turon X, Riesgo A. Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchinArbacia lixulausing RNA-seq. Mol Ecol Resour 2015; 16:794-808. [DOI: 10.1111/1755-0998.12500] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/26/2022]
Affiliation(s)
- R. Pérez-Portela
- Center for Advanced Studies of Blanes (CEAB-CSIC); Acceso a la Cala Sant Francesc 14 17300 Girona Spain
- Department of Animal Biology; University of Barcelona; 643 Diagonal Avenue 08028 Barcelona Spain
| | - X. Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC); Acceso a la Cala Sant Francesc 14 17300 Girona Spain
| | - A. Riesgo
- Department of Animal Biology; University of Barcelona; 643 Diagonal Avenue 08028 Barcelona Spain
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Lai KP, Li JW, Gu J, Chan TF, Tse WKF, Wong CKC. Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel. BMC Genomics 2015; 16:1072. [PMID: 26678671 PMCID: PMC4683740 DOI: 10.1186/s12864-015-2271-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homeostasis of ions and water is important for the maintenance of cellular functions. The regulation of the homeostasis is particularly important in euryhaline fish that migrate between freshwater (FW) and seawater (SW) environments. The fish gill, the major tissue that forms an interface separating the extracellular fluids and external water environment, has an effective transport system to maintain and regulate a constant body osmolality. In fish gills, the two major epithelial cells, pavement cells (PVCs) and mitochondria-rich cells (MRCs), are known to play key and complementary roles in ion transport at the interface. Discovering the robust mechanisms underlying the two cell types' response to osmotic stress would benefit our understanding of the fundamental mechanism allowing PVCs and MRCs to handle osmotic stress. Owing to the limited genomic data available on estuarine species, existing knowledge in this area is slim. In this study, transcriptome analyses were conducted using PVCs and MRCs isolated from Japanese eels adapted to FW or SW environments to provide a genome-wide molecular study to unravel the fundamental processes at work. RESULTS The study identified more than 12,000 transcripts in the gill cells. Interestingly, remarkable differential expressed genes (DEGs) were identified in PVCs (970 transcripts) instead of MRCs (400 transcripts) in gills of fish adapted to FW or SW. Since PVCs cover more than 90 % of the gill epithelial surface, the greater change in gene expression patterns in PVCs in response to external osmolality is anticipated. In the integrity pathway analysis, 19 common biological functions were identified in PVCs and MRCs. In the enriched signaling pathways analysis, most pathways differed between PVCs and MRCs; 14 enriched pathways were identified in PVCs and 12 in MRCs. The results suggest that the osmoregulatory responses in PVCs and MRCs are cell-type specific, which supports the complementary functions of the cells in osmoregulation. CONCLUSIONS This is the first study to provide transcriptomic analysis of PVCs and MRCs in gills of eels adapted to FW or SW environments. It describes the cell-type specific transcriptomic network in different tonicity. The findings consolidate the known osmoregulatory pathways and provide molecular insight in osmoregulation. The presented data will be useful for researchers to select their targets for further studies.
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Affiliation(s)
- Keng Po Lai
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Jing-Woei Li
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Je Gu
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - William Ka Fai Tse
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong. .,Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Pok Fu Lam, Hong Kong.
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De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing. GENETICS RESEARCH INTERNATIONAL 2015; 2015:638679. [PMID: 26788372 PMCID: PMC4695645 DOI: 10.1155/2015/638679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/29/2023]
Abstract
We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.
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Abstract
Winged insects underwent an unparalleled evolutionary radiation, but mechanisms underlying the origin and diversification of wings in basal insects are sparsely known compared with more derived holometabolous insects. In the neopteran species Oncopeltus fasciatus, we manipulated wing specification genes and used RNA-seq to obtain both functional and genomic perspectives. Combined with previous studies, our results suggest the following key steps in wing origin and diversification. First, a set of dorsally derived outgrowths evolved along a number of body segments including the first thoracic segment (T1). Homeotic genes were subsequently co-opted to suppress growth of some dorsal flaps in the thorax and abdomen. In T1 this suppression was accomplished by Sex combs reduced, that when experimentally removed, results in an ectopic T1 flap similar to prothoracic winglets present in fossil hemipteroids and other early insects. Global gene-expression differences in ectopic T1 vs. T2/T3 wings suggest that the transition from flaps to wings required ventrally originating cells, homologous with those in ancestral arthropod gill flaps/epipods, to migrate dorsally and fuse with the dorsal flap tissue thereby bringing new functional gene networks; these presumably enabled the T2/T3 wing's increased size and functionality. Third, "fused" wings became both the wing blade and surrounding regions of the dorsal thorax cuticle, providing tissue for subsequent modifications including wing folding and the fit of folded wings. Finally, Ultrabithorax was co-opted to uncouple the morphology of T2 and T3 wings and to act as a general modifier of hindwings, which in turn governed the subsequent diversification of lineage-specific wing forms.
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Petrella V, Aceto S, Musacchia F, Colonna V, Robinson M, Benes V, Cicotti G, Bongiorno G, Gradoni L, Volf P, Salvemini M. De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum. BMC Genomics 2015; 16:847. [PMID: 26493315 PMCID: PMC4619268 DOI: 10.1186/s12864-015-2088-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/15/2015] [Indexed: 12/17/2022] Open
Abstract
Background The phlebotomine sand fly Phlebotomus perniciosus (Diptera: Psychodidae, Phlebotominae) is a major Old World vector of the protozoan Leishmania infantum, the etiological agent of visceral and cutaneous leishmaniases in humans and dogs, a worldwide re-emerging diseases of great public health concern, affecting 101 countries. Despite the growing interest in the study of this sand fly species in the last years, the development of genomic resources has been limited so far. To increase the available sequence data for P. perniciosus and to start studying the molecular basis of the sexual differentiation in sand flies, we performed whole transcriptome Illumina RNA sequencing (RNA-seq) of adult males and females and de novo transcriptome assembly. Results We assembled 55,393 high quality transcripts, of which 29,292 were unique, starting from adult whole body male and female pools. 11,736 transcripts had at least one functional annotation, including full-length low abundance salivary transcripts, 981 transcripts were classified as putative long non-coding RNAs and 244 transcripts encoded for putative novel proteins specific of the Phlebotominae sub-family. Differential expression analysis identified 8590 transcripts significantly biased between sexes. Among them, some show relaxation of selective constraints when compared to their orthologs of the New World sand fly species Lutzomyia longipalpis. Conclusions In this paper, we present a comprehensive transcriptome resource for the sand fly species P. perniciosus built from short-read RNA-seq and we provide insights into sex-specific gene expression at adult stage. Our analysis represents a first step towards the identification of sex-specific genes and pathways and a foundation for forthcoming investigations into this important vector species, including the study of the evolution of sex-biased genes and of the sexual differentiation in phlebotomine sand flies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2088-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V Petrella
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - S Aceto
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - F Musacchia
- Stazione Zoologica "Anton Dohrn", Naples, Italy
| | - V Colonna
- National Research Council, Institute of Genetics and Biophysics, Naples, Italy
| | - M Robinson
- Institute of Molecular Life Science, University of Zurich, Zurich, Switzerland.,SIB-Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - V Benes
- Genomics Core Facility, EMBL, Heidelberg, Germany
| | - G Cicotti
- Institute for High Performance Computing and Networking, ICAR-CNR, Naples, Italy
| | - G Bongiorno
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - L Gradoni
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - P Volf
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - M Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy.
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Transcriptome Changes during the Life Cycle of the Red Sponge, Mycale phyllophila (Porifera, Demospongiae, Poecilosclerida). Genes (Basel) 2015; 6:1023-52. [PMID: 26492274 PMCID: PMC4690027 DOI: 10.3390/genes6041023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/14/2015] [Accepted: 09/29/2015] [Indexed: 01/10/2023] Open
Abstract
Sponges are an ancient metazoan group with broad ecological, evolutionary, and biotechnological importance. As in other marine invertebrates with a biphasic life cycle, the developing sponge undergoes a significant morphological, physiological, and ecological transformation during settlement and metamorphosis. In this study, we compare new transcriptome datasets for three life cycle stages of the red sponge (Mycale phyllophila) to test whether gene expression (as in the model poriferan, Amphimedon queenslandica) also varies more after settlement and metamorphosis. In contrast to A. queenslandica, we find that the transcriptome of M. phyllophila changes more during the earlier pre-competent larva/post-larva transition that spans these defining events. We also find that this transition is marked by a greater frequency of significantly up-regulated Gene Ontology terms including those for morphogenesis, differentiation, and development and that the transcriptomes of its pre-competent larvae and adult are distinct. The life cycle transcriptome variation between M. phyllophila and A. queenslandica may be due to their long separate evolutionary histories and corresponding differences in developmental rates and timing. This study now calls for new transcriptome datasets of M. phyllophila and other sponges, which will allow for tests of the generality of our life cycle expression differences and for the greater exploitation of poriferans in both basic and applied research.
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Whittle CA, Extavour CG. Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea. G3 (BETHESDA, MD.) 2015; 5:2307-21. [PMID: 26384771 PMCID: PMC4632051 DOI: 10.1534/g3.115.021402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/28/2015] [Indexed: 01/24/2023]
Abstract
In protein-coding genes, synonymous codon usage and amino acid composition correlate to expression in some eukaryotes, and may result from translational selection. Here, we studied large-scale RNA-seq data from three divergent arthropod models, including cricket (Gryllus bimaculatus), milkweed bug (Oncopeltus fasciatus), and the amphipod crustacean Parhyale hawaiensis, and tested for optimization of codon and amino acid usage relative to expression level. We report strong signals of AT3 optimal codons (those favored in highly expressed genes) in G. bimaculatus and O. fasciatus, whereas weaker signs of GC3 optimal codons were found in P. hawaiensis, suggesting selection on codon usage in all three organisms. Further, in G. bimaculatus and O. fasciatus, high expression was associated with lowered frequency of amino acids with large size/complexity (S/C) scores in favor of those with intermediate S/C values; thus, selection may favor smaller amino acids while retaining those of moderate size for protein stability or conformation. In P. hawaiensis, highly transcribed genes had elevated frequency of amino acids with large and small S/C scores, suggesting a complex dynamic in this crustacean. In all species, the highly transcribed genes appeared to favor short proteins, high optimal codon usage, specific amino acids, and were preferentially involved in cell-cycling and protein synthesis. Together, based on examination of 1,680,067, 1,667,783, and 1,326,896 codon sites in G. bimaculatus, O. fasciatus, and P. hawaiensis, respectively, we conclude that translational selection shapes codon and amino acid usage in these three Pancrustacean arthropods.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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Lavore A, Pascual A, Salinas FM, Esponda-Behrens N, Martinez-Barnetche J, Rodriguez M, Rivera-Pomar R. Comparative analysis of zygotic developmental genes in Rhodnius prolixus genome shows conserved features on the tracheal developmental pathway. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 64:32-43. [PMID: 26187251 DOI: 10.1016/j.ibmb.2015.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 06/13/2015] [Accepted: 06/21/2015] [Indexed: 06/04/2023]
Abstract
Most of the in-depth studies on insect developmental genetic have been carried out in the fruit fly Drosophila melanogaster, an holometabolous insect, so much more still remains to be studied in hemimetabolous insects. Having Rhodnius prolixus sequenced genome available, we search for orthologue genes of zygotic signaling pathways, segmentation, and tracheogenesis in the R. prolixus genome and in three species of Triatoma genus transcriptomes, concluding that there is a high level of gene conservation. We also study the function of two genes required for tracheal system development in D. melanogaster - R. prolixus orthologues: trachealess (Rp-trh) and empty spiracles (Rp-ems). From that we see that Rp-trh is required for early tracheal development since Rp-trh RNAi shows that the primary tracheal branches fail to form. On the other hand, Rp-ems is implied in the proper formation of the posterior tracheal branches, in a similar way to D. melanogaster. These results represent the initial characterization of the genes involved in the tracheal development of an hemimetabolous insect building a bridge between the current genomic era and V. Wigglesworth's classical studies on insects' respiratory system physiology.
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Affiliation(s)
- A Lavore
- Centro de Bioinvestigaciones and Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Monteagudo 2772, 2700, Pergamino, Buenos Aires, Argentina.
| | - A Pascual
- Centro de Bioinvestigaciones and Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Monteagudo 2772, 2700, Pergamino, Buenos Aires, Argentina; Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Bvd 120 y 62, La Plata, Buenos Aires, Argentina.
| | - F M Salinas
- Centro de Bioinvestigaciones and Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Monteagudo 2772, 2700, Pergamino, Buenos Aires, Argentina.
| | - N Esponda-Behrens
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Bvd 120 y 62, La Plata, Buenos Aires, Argentina.
| | - J Martinez-Barnetche
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Sta. María Ahuacatitlán, Cuernavaca, Mexico.
| | - M Rodriguez
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Sta. María Ahuacatitlán, Cuernavaca, Mexico.
| | - R Rivera-Pomar
- Centro de Bioinvestigaciones and Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Monteagudo 2772, 2700, Pergamino, Buenos Aires, Argentina; Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Bvd 120 y 62, La Plata, Buenos Aires, Argentina.
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Perera OP, Shelby KS, Popham HJR, Gould F, Adang MJ, Jurat-Fuentes JL. Generation of a Transcriptome in a Model Lepidopteran Pest, Heliothis virescens, Using Multiple Sequencing Strategies for Profiling Midgut Gene Expression. PLoS One 2015; 10:e0128563. [PMID: 26047101 PMCID: PMC4457788 DOI: 10.1371/journal.pone.0128563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 04/29/2015] [Indexed: 02/04/2023] Open
Abstract
Heliothine pests such as the tobacco budworm, Heliothis virescens (F.), pose a significant threat to production of a variety of crops and ornamental plants and are models for developmental and physiological studies. The efforts to develop new control measures for H. virescens, as well as its use as a relevant biological model, are hampered by a lack of molecular resources. The present work demonstrates the utility of next-generation sequencing technologies for rapid molecular resource generation from this species for which lacks a sequenced genome. In order to amass a de novo transcriptome for this moth, transcript sequences generated from Illumina, Roche 454, and Sanger sequencing platforms were merged into a single de novo transcriptome assembly. This pooling strategy allowed a thorough sampling of transcripts produced under diverse environmental conditions, developmental stages, tissues, and infections with entomopathogens used for biological control, to provide the most complete transcriptome to date for this species. Over 138 million reads from the three platforms were assembled into the final set of 63,648 contigs. Of these, 29,978 had significant BLAST scores indicating orthologous relationships to transcripts of other insect species, with the top-hit species being the monarch butterfly (Danaus plexippus) and silkworm (Bombyx mori). Among identified H. virescens orthologs were immune effectors, signal transduction pathways, olfactory receptors, hormone biosynthetic pathways, peptide hormones and their receptors, digestive enzymes, and insecticide resistance enzymes. As an example, we demonstrate the utility of this transcriptomic resource to study gene expression profiling of larval midguts and detect transcripts of putative Bacillus thuringiensis (Bt) Cry toxin receptors. The substantial molecular resources described in this study will facilitate development of H. virescens as a relevant biological model for functional genomics and for new biological experimentation needed to develop efficient control efforts for this and related Noctuid pest moths.
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Affiliation(s)
- Omaththage P. Perera
- Southern Insect Management Research Unit, USDA, Agricultural Research Service, Stoneville, MS, 38776, United States of America
| | - Kent S. Shelby
- Biological Control of Insects Research Laboratory, USDA, Agricultural Research Service, Columbia, Missouri, 65203, United States of America
| | - Holly J. R. Popham
- Biological Control of Insects Research Laboratory, USDA, Agricultural Research Service, Columbia, Missouri, 65203, United States of America
| | - Fred Gould
- Dept. Entomology, North Carolina State University, Raleigh, NC, 27607, United States of America
| | - Michael J. Adang
- Dept. Entomology, University of Georgia, Athens, GA, 30602, United States of America
| | - Juan Luis Jurat-Fuentes
- Dept. Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, United States of America
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Sachs L, Chen YT, Drechsler A, Lynch JA, Panfilio KA, Lässig M, Berg J, Roth S. Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insect. eLife 2015; 4:e05502. [PMID: 25962855 PMCID: PMC4423117 DOI: 10.7554/elife.05502] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/12/2015] [Indexed: 11/13/2022] Open
Abstract
Toll-dependent patterning of the dorsoventral axis in Drosophila represents one of the best understood gene regulatory networks. However, its evolutionary origin has remained elusive. Outside the insects Toll is not known for a patterning function, but rather for a role in pathogen defense. Here, we show that in the milkweed bug Oncopeltus fasciatus, whose lineage split from Drosophila's more than 350 million years ago, Toll is only required to polarize a dynamic BMP signaling network. A theoretical model reveals that this network has self-regulatory properties and that shallow Toll signaling gradients are sufficient to initiate axis formation. Such gradients can account for the experimentally observed twinning of insect embryos upon egg fragmentation and might have evolved from a state of uniform Toll activity associated with protecting insect eggs against pathogens.
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Affiliation(s)
- Lena Sachs
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Yen-Ta Chen
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Axel Drechsler
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- Bundesministerium für Umwelt, Naturschutz, Bau und Reaktorsicherheit, Bonn, Germany
| | - Jeremy A Lynch
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States
| | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Michael Lässig
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Johannes Berg
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Siegfried Roth
- Institute for Developmental Biology, University of Cologne, Köln, Germany
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Transcriptomic responses of corpuscle of Stannius gland of Japanese eels (Anguilla japonica) to changes in water salinity. Sci Rep 2015; 5:9836. [PMID: 25907828 PMCID: PMC5386212 DOI: 10.1038/srep09836] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/19/2015] [Indexed: 12/23/2022] Open
Abstract
Physiological studies of a unique endocrine gland in fish, named corpuscles of Stannius (CS), described a Ca2(+)-regulatory function for this gland mediated by stanniocalcin-1, a hypocalcemic polypeptide hormone. However, to date, the endocrine functions of the glands have not been completely elucidated.We hypothesized that other unidentified active principles in the glands are involved in the regulation of plasma ion (Na(+), Ca2(+)) and/or blood pressure. In this study, transcriptome sequencing of CS glands was performed using Japanese eels (Anguilla japonica) adapted to freshwater (FW) or seawater (SW) to reveal the presence and differential expression of genes encoding proteins related to the ion-osmoregulatory and pressor functions. We acquired a total of 14.1 Mb and 12.1 Mb quality-trimmed reads from the CS glands collected from FW and SW adapted eels, respectively. The de novo assembly resulted in 9254 annotated genes. Among them, 475 genes were differentially expressed with 357 up- and 118 down-regulated in the SW group. Gene ontology analysis further demonstrated the presence of natriuresis and pressor related genes. In summary, ours is the first study using high-throughput sequencing to identify gene targets that could explain the physiological importance of the CS glands.
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Oppenheim SJ, Baker RH, Simon S, DeSalle R. We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects. INSECT MOLECULAR BIOLOGY 2015; 24:139-54. [PMID: 25524309 PMCID: PMC4383654 DOI: 10.1111/imb.12154] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Insects are the most diverse group of organisms on the planet. Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa. Increasingly, studies are using a comparative approach (across species, sexes and life stages) that examines the transcriptional basis of phenotypic diversity within an evolutionary context. In the present review, we summarize much of this research, focusing in particular on three critical aspects of insect biology: morphological development and plasticity; physiological response to the environment; and sexual dimorphism. A common feature that is emerging from these investigations concerns the dynamic nature of transcriptome evolution as indicated by rapid changes in the overall pattern of gene expression, the differential expression of numerous genes with unknown function, and the incorporation of novel, lineage-specific genes into the transcriptional profile.
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Affiliation(s)
- Sara J Oppenheim
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
| | - Richard H Baker
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
| | - Sabrina Simon
- Biosystematics Group, Wageningen UniversityWageningen, The Netherlands
| | - Rob DeSalle
- Department of Entomology, Division of Invertebrates, Sackler Institute for Comparative Genomics, American Museum of Natural HistoryNew York, NY, USA
- Correspondence: Dr. Robert DeSalle, Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA. Tel.: 212-769-5670; e-mail:
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45
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Lai KP, Li JW, Wang SY, Chiu JMY, Tse A, Lau K, Lok S, Au DWT, Tse WKF, Wong CKC, Chan TF, Kong RYC, Wu RSS. Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. BMC Genomics 2015; 16:135. [PMID: 25765076 PMCID: PMC4352242 DOI: 10.1186/s12864-015-1325-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/06/2015] [Indexed: 11/12/2022] Open
Abstract
Background The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melastigma in the assessment of in vivo molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although O. melastigma is believed to be phylogenetically closely related to Oryzias latipes, the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by de novo assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of O. melastigma. We also investigated the possible extent of divergence between O. melastigma and O. latipes at the transcriptome level. Results More than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between O. melastigma and O. latipes. Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma. Conclusions Orthologous transcripts between O. melastigma and O. latipes, tissue-enriched genes and O. melastigma-enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing in vivo molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1325-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keng Po Lai
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Jing-Woei Li
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - Simon Yuan Wang
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Jill Man-Ying Chiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Anna Tse
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Karen Lau
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Si Lok
- Genome Research Centre, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, 5 Sassoon Road, Pokfulam, Hong Kong, SAR, China.
| | - Doris Wai-Ting Au
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - William Ka-Fai Tse
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China.
| | - Chris Kong-Chu Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Ting-Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, SAR, China.
| | - Richard Yuen-Chong Kong
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
| | - Rudolf Shiu-Sun Wu
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. .,The State Key Laboratory in Marine Pollution, Hong Kong, China.
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de Assis Fonseca FC, Firmino AAP, de Macedo LLP, Coelho RR, de Sousa Júnior JDA, Silva-Junior OB, Togawa RC, Pappas GJ, de Góis LAB, da Silva MCM, Grossi-de-Sá MF. Sugarcane giant borer transcriptome analysis and identification of genes related to digestion. PLoS One 2015; 10:e0118231. [PMID: 25706301 PMCID: PMC4338194 DOI: 10.1371/journal.pone.0118231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/11/2015] [Indexed: 11/25/2022] Open
Abstract
Sugarcane is a widely cultivated plant that serves primarily as a source of sugar and ethanol. Its annual yield can be significantly reduced by the action of several insect pests including the sugarcane giant borer (Telchin licus licus), a lepidopteran that presents a long life cycle and which efforts to control it using pesticides have been inefficient. Although its economical relevance, only a few DNA sequences are available for this species in the GenBank. Pyrosequencing technology was used to investigate the transcriptome of several developmental stages of the insect. To maximize transcript diversity, a pool of total RNA was extracted from whole body insects and used to construct a normalized cDNA database. Sequencing produced over 650,000 reads, which were de novo assembled to generate a reference library of 23,824 contigs. After quality score and annotation, 43% of the contigs had at least one BLAST hit against the NCBI non-redundant database, and 40% showed similarities with the lepidopteran Bombyx mori. In a further analysis, we conducted a comparison with Manduca sexta midgut sequences to identify transcripts of genes involved in digestion. Of these transcripts, many presented an expansion or depletion in gene number, compared to B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of aminopeptidase N (APN) cDNAs were characterized based on homology to those reported as Cry toxin receptors. This is the first report that provides a large-scale EST database for the species. Transcriptome analysis will certainly be useful to identify novel developmental genes, to better understand the insect's biology and to guide the development of new strategies for insect-pest control.
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Affiliation(s)
- Fernando Campos de Assis Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Alexandre Augusto Pereira Firmino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Lima Pepino de Macedo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Roberta Ramos Coelho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | - Orzenil Bonfim Silva-Junior
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Maria Fátima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
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Salvemini M, Arunkumar KP, Nagaraju J, Sanges R, Petrella V, Tomar A, Zhang H, Zheng W, Saccone G. De novo assembly and transcriptome analysis of the Mediterranean fruit fly Ceratitis capitata early embryos. PLoS One 2014; 9:e114191. [PMID: 25474564 PMCID: PMC4256415 DOI: 10.1371/journal.pone.0114191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/05/2014] [Indexed: 01/04/2023] Open
Abstract
The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of other damaging pest species. The Medfly has been the first non-drosophilid fly species which has been genetically transformed paving the way for designing genetic-based pest control strategies. Furthermore, it is an experimentally tractable model, in which transient and transgene-mediated RNAi have been successfully used. We applied Illumina sequencing to total RNA preparations of 8–10 hours old embryos of C. capitata, This developmental window corresponds to the blastoderm cellularization stage. In summary, we assembled 42,614 transcripts which cluster in 26,319 unique transcripts of which 11,045 correspond to protein coding genes; we identified several hundreds of long ncRNAs; we found an enrichment of transcripts encoding RNA binding proteins among the highly expressed transcripts, such as CcTRA-2, known to be necessary to establish and, most likely, to maintain female sex of C. capitata. Our study is the first de novo assembly performed for Ceratitis capitata based on Illumina NGS technology during embryogenesis and it adds novel data to the previously published C. capitata EST databases. We expect that it will be useful for a variety of applications such as gene cloning and phylogenetic analyses, as well as to advance genetic research and biotechnological applications in the Medfly and other related Tephritidae.
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Affiliation(s)
- Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | | | - Remo Sanges
- Stazione Zoologica "Anton Dohrn", Naples, Italy
| | - Valeria Petrella
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Archana Tomar
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Hongyu Zhang
- State Key Laboratory of Agricultural Microbiology and Institute of Urban and Horticultural Pests, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Weiwei Zheng
- State Key Laboratory of Agricultural Microbiology and Institute of Urban and Horticultural Pests, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Giuseppe Saccone
- Department of Biology, University of Naples Federico II, Naples, Italy
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48
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Nuñez Ortiz N, Gerdol M, Stocchi V, Marozzi C, Randelli E, Bernini C, Buonocore F, Picchietti S, Papeschi C, Sood N, Pallavicini A, Scapigliati G. T cell transcripts and T cell activities in the gills of the teleost fish sea bass (Dicentrarchus labrax). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 47:309-318. [PMID: 25109574 DOI: 10.1016/j.dci.2014.07.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/23/2014] [Accepted: 07/23/2014] [Indexed: 06/03/2023]
Abstract
The gills of fish are a mucosal tissue that contains T cells involved in the recognition of non-self and pathogens, and in this work we describe some features of gill-associated T cells of European sea bass, a marine model species. A whole transcriptome was obtained by deep sequencing of RNA from unstimulated gills that has been analyzed for the presence of T cell-related transcripts. Of the putative expressed sequences identified in the transcriptome, around 30 were related to main functions related to T cells including Th1/Th2/Th17/Treg cell subpopulations, thus suggesting their possible presence in the branchial epithelium. The number of T cells in the gills of sea bass, measured with the specific T cell mAb DLT15 range from 10% to 20%, and IHC analysis shows their abundance and distribution in the epithelium. Leukocytes from gills are able to proliferate in the presence of lectins ConA and PHA, as measured by flow cytometry using CFSE fluorescence incorporation, and during proliferation the number of T cells counted by immunofluorescence increased. In lectin-proliferating cells the expression of T cell-related genes TRβ, TRγ, CD4, CD8α, CD45 and IL-10 increased dramatically. Our data represent a first analysis on T cell genes and on basic T cell activities of fish gills, and suggest the presence of functionally active subpopulations of T lymphocytes in this tissue.
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MESH Headings
- Animals
- Bass/genetics
- Bass/immunology
- Cell Proliferation/drug effects
- Concanavalin A/pharmacology
- Fish Proteins/genetics
- Fish Proteins/immunology
- Gene Expression Profiling
- Gene Expression Regulation
- Gills/cytology
- Gills/immunology
- Gills/metabolism
- Immunity, Mucosal
- Immunophenotyping
- Molecular Sequence Annotation
- Phytohemagglutinins/pharmacology
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Th1 Cells/cytology
- Th1 Cells/immunology
- Th1 Cells/metabolism
- Th17 Cells/cytology
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Th2 Cells/cytology
- Th2 Cells/immunology
- Th2 Cells/metabolism
- Transcriptome/genetics
- Transcriptome/immunology
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Affiliation(s)
- N Nuñez Ortiz
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - M Gerdol
- Dipartimento di Scienze della Vita, Università di Trieste, Italy
| | - V Stocchi
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - C Marozzi
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - E Randelli
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - C Bernini
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - F Buonocore
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - S Picchietti
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - C Papeschi
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy
| | - N Sood
- National Bureau of Fish Genetic Resources, Lucknow, UP, India
| | - A Pallavicini
- Dipartimento di Scienze della Vita, Università di Trieste, Italy
| | - G Scapigliati
- Dipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali, Università della Tuscia, Italy.
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49
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Zhao X, Yu H, Kong L, Liu S, Li Q. Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PLoS One 2014; 9:e111915. [PMID: 25369077 PMCID: PMC4219811 DOI: 10.1371/journal.pone.0111915] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022] Open
Abstract
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.
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Affiliation(s)
- Xuelin Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
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50
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Gerdol M, De Moro G, Manfrin C, Milandri A, Riccardi E, Beran A, Venier P, Pallavicini A. RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. BMC Res Notes 2014; 7:722. [PMID: 25314922 PMCID: PMC4203926 DOI: 10.1186/1756-0500-7-722] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
Background The Mediterranean mussel Mytilus galloprovincialis is marine bivalve with a relevant commercial importance as well as a key sentinel organism for the biomonitoring of environmental pollution. Here we report the RNA sequencing of the mussel digestive gland, performed with the aim: a) to produce a high quality de novo transcriptome assembly, thus improving the genetic and molecular knowledge of this organism b) to provide an initial assessment of the response to paralytic shellfish poisoning (PSP) on a molecular level, in order to identify possible molecular markers of toxin accumulation. Results The comprehensive de novo assembly and annotation of the transcriptome yielded a collection of 12,079 non-redundant consensus sequences with an average length of 958 bp, with a high percentage of full-length transcripts. The whole-transcriptome gene expression study indicated that the accumulation of paralytic toxins produced by the dinoflagellate Alexandrium minutum over a time span of 5 days scarcely affected gene expression, but the results need further validation with a greater number of biological samples and naturally contaminated specimens. Conclusion The digestive gland reference transcriptome we produced significantly improves the data collected from previous sequencing efforts and provides a basic resource for expanding functional genomics investigations in M. galloprovincialis. Although not conclusive, the results of the RNA-seq gene expression analysis support the classification of mussels as bivalves refractory to paralytic shellfish poisoning and point out that the identification molecular biomarkers of PSP in the digestive gland of this organism is problematic. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-722) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Alberto Pallavicini
- Laboratory of Genetics, Department of Life Sciences, University of Trieste, Via Licio Giorgeri 5, Trieste 34126, Italy.
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