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Saha B, McNinch CM, Lu S, Ho MCW, De Carvalho SS, Barillas-Mury C. In-depth transcriptomic analysis of Anopheles gambiae hemocytes uncovers novel genes and the oenocytoid developmental lineage. BMC Genomics 2024; 25:80. [PMID: 38243165 PMCID: PMC10799387 DOI: 10.1186/s12864-024-09986-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/07/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Hemocytes are immune cells that patrol the mosquito hemocoel and mediate critical cellular defense responses against pathogens. However, despite their importance, a comprehensive transcriptome of these cells was lacking because they constitute a very small fraction of the total cells in the insect, limiting the study of hemocyte differentiation and immune function. RESULTS In this study, an in-depth hemocyte transcriptome was built by extensive bulk RNA sequencing and assembly of hemocyte RNAs from adult A. gambiae female mosquitoes, based on approximately 2.4 billion short Illumina and about 9.4 million long PacBio high-quality reads that mapped to the A. gambiae PEST genome (P4.14 version). A total of 34,939 transcripts were annotated including 4,020 transcripts from novel genes and 20,008 novel isoforms that result from extensive differential splicing of transcripts from previously annotated genes. Most hemocyte transcripts identified (89.8%) are protein-coding while 10.2% are non-coding RNAs. The number of transcripts identified in the novel hemocyte transcriptome is twice the number in the current annotation of the A. gambiae genome (P4.14 version). Furthermore, we were able to refine the analysis of a previously published single-cell transcriptome (scRNAseq) data set by using the novel hemocyte transcriptome as a reference to re-define the hemocyte clusters and determine the path of hemocyte differentiation. Unsupervised pseudo-temporal ordering using the Tools for Single Cell Analysis software uncovered a novel putative prohemocyte precursor cell type that gives rise to prohemocytes. Pseudo-temporal ordering with the Monocle 3 software, which analyses changes in gene expression during dynamic biological processes, determined that oenocytoids derive from prohemocytes, a cell population that also gives rise to the granulocyte lineage. CONCLUSION A high number of mRNA splice variants are expressed in hemocytes, and they may account for the plasticity required to mount efficient responses to many different pathogens. This study highlights the importance of a comprehensive set of reference transcripts to perform robust single-cell transcriptomic data analysis of cells present in low abundance. The detailed annotation of the hemocyte transcriptome will uncover new facets of hemocyte development and function in adult dipterans and is a valuable community resource for future studies on mosquito cellular immunity.
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Affiliation(s)
- Banhisikha Saha
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Colton M McNinch
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephen Lu
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Margaret C W Ho
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephanie Serafim De Carvalho
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA.
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Pezenti LF, Dionisio JF, Sosa-Gómez DR, de Souza RF, da Rosa R. Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Genome 2023. [DOI: 10.1139/gen-2022-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis ( Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.
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Powell D, Ngo PT, Nguyen HN, Knibb W, Elizur A. Transcriptomic responses of saline-adapted Nile tilapia (Oreochromis niloticus) to rearing in both saline and freshwater. Mar Genomics 2021; 60:100879. [PMID: 34023275 DOI: 10.1016/j.margen.2021.100879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 03/26/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022]
Abstract
The Nile tilapia, Oreochromis niloticus, is an important species for global aquaculture. Recently, a single genetic line of Nile tilapia was developed using estimated breeding values (EBVs) for body weight under moderately saline water that showed significant improvement in growth performance. To explore the molecular mechanisms underlying this enhanced growth capacity, RNA-Seq was used to profile differences in gene expression in the liver and pituitary gland of high- and low-growth performance families of male Nile tilapia progeny, reared in either saline or freshwater environments. Comparisons of tissues from high- and low-EBV families, and also between fish reared in either saline or freshwater, revealed 142 and 2208 differentially expressed genes (DEGs), respectively. DEGs identified between the EBV groups comprised a number of genes involved in the regulation of growth and reproduction. We found an overexpression of hormone genes involved in growth-inhibition in the pituitary of Low-EBV tilapia including 2 somatostatin genes (GHIH), corticoliberin (CRH) and tachykinin-3-like protein. Furthermore, several genes associated with the cAMP pathway were underexpressed in low-EBV tilapia pituitary together with several early response genes. This study provides insight into the transcriptomic factors associated with growth performance in saline-adapted Nile tilapia reared in environments with high and low salinity levels and provides valuable knowledge for the future development of selection strategies to improve growth performance in this species.
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Affiliation(s)
- Daniel Powell
- Department of Biology, Lund University, 223 62 Lund, Sweden; Centre for Genetics, Ecology and Physiology, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
| | - Phu Thoa Ngo
- Centre for Genetics, Ecology and Physiology, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia; Mavin Aquaculture, Mavin Group, Hudland Tower Building, No. 6 Nguyen Huu Tho, Hoang Liet Ward, Hoang Mai District, Hanoi, Viet Nam; Research Institute for Aquaculture No.1, Dinh Bang, Tu Son, Bac Ninh, Viet Nam.
| | - Hong Nguyen Nguyen
- Centre for Genetics, Ecology and Physiology, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
| | - Wayne Knibb
- Centre for Genetics, Ecology and Physiology, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
| | - Abigail Elizur
- Centre for Genetics, Ecology and Physiology, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
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Li D, Zhang C, Tong Z, Su D, Zhang G, Zhang S, Zhao H, Hu Z. Transcriptome response comparison between vector and non-vector aphids after feeding on virus-infected wheat plants. BMC Genomics 2020; 21:638. [PMID: 32933469 PMCID: PMC7493910 DOI: 10.1186/s12864-020-07057-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/06/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Plant viruses maintain intricate interactions with their vector and non-vector insects and can impact the fitness of insects. However, the details of their molecular and cellular mechanisms have not been studied well. We compared the transcriptome-level responses in vector and non-vector aphids (Schizaphis graminum and Rhopalosiphum padi, respectively) after feeding on wheat plants with viral infections (Barley Yellow Dwarf Virus (BYDV) and Wheat dwarf virus (WDV), respectively). We conducted differentially expressed gene (DEG) annotation analyses and observed DEGs related to immune pathway, growth, development, and reproduction. And we conducted cloning and bioinformatic analyses of the key DEG involved in immune. RESULTS For all differentially expressed gene analyses, the numbers of DEGs related to immune, growth, development, reproduction and cuticle were higher in vector aphids than in non-vector aphids. STAT5B (signal transducer and activator of transcription 5B), which is involved in the JAK-STAT pathway, was upregulated in R. padi exposed to WDV. The cloning and bioinformatic results indicated that the RpSTAT5B sequence contains a 2082 bp ORF encoding 693 amino acids. The protein molecular weight is 79.1 kD and pI is 8.13. Analysis indicated that RpSTAT5B is a non-transmembrane protein and a non-secreted protein. Homology and evolutionary analysis indicated that RpSTAT5B was closely related to R. maidis. CONCLUSIONS Unigene expression analysis showed that the total number of differentially expressed genes (DEGs) in the vector aphids was higher than that in the non-vector aphids. Functional enrichment analysis showed that the DEGs related to immunity, growth and reproduction in vector aphids were higher than those in non-vector aphids, and the differentially expressed genes related to immune were up-regulated. This study provides a basis for the evaluation of the response mechanisms of vector/non-vector insects to plant viruses.
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Affiliation(s)
- Dandan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Chi Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zeqian Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Dan Su
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Gaisheng Zhang
- Ministry of Education, Key Laboratory of Crop Heterosis of Shaanxi Province, National Yangling Agricultural Biotechnology and Breeding Center, Yangling Branch of State Wheat Improvement Centre/Wheat Breeding Engineering Research Center, Northwest A&F University, Yangling, China
| | - Shize Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Huiyan Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zuqing Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China.
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5
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Semmouri I, De Schamphelaere KAC, Van Nieuwerburgh F, Deforce D, Janssen CR, Asselman J. Spatio-temporal patterns in the gene expression of the calanoid copepod Temora longicornis in the Belgian part of the North Sea. MARINE ENVIRONMENTAL RESEARCH 2020; 160:105037. [PMID: 32907738 DOI: 10.1016/j.marenvres.2020.105037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Marine zooplankton are increasingly being affected by recent environmental changes, such as climate change, and respond with profound spatial relocations and shifts in phenology and physiology. In order to predict whether populations are able to persist or adapt to such new conditions, it is essential to understand the molecular basis of such adaptations, which ultimately get translated into these physiological responses. To explore variation in population gene expression across time and space, we investigated transcriptome-level profiles of the calanoid copepod Temora longicornis, that were collected at four different locations in the Belgian Part of the North Sea (BPNS) on three different time points (April, June, October) in 2018. RNA-seq analysis of field collected adults identified large seasonal differences in gene expression, mainly between spring-summer and autumn samples. The largest log-fold changes occurred in a set of genes encoding for ribosomal and myosin (heavy chain) transcripts. Enrichment analysis revealed a strong seasonal pattern in vitellogenin, cuticle and glycolytic gene expression as well. We also found a positive correlation between vitellogenin expression and densities of T. longicornis. No clear spatial variation in expression patterns was found in the BPNS. This study underlines the potential of field gene expression studies for biomonitoring purposes and the significance of considering seasonal variation in future studies.
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Affiliation(s)
- Ilias Semmouri
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium.
| | - Karel A C De Schamphelaere
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, 9000, Ghent, Belgium
| | - Dieter Deforce
- Ghent University, Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, 9000, Ghent, Belgium
| | - Colin R Janssen
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium; Blue Growth Research Lab, Ghent University, Bluebridge, Wetenschapspark 1, 8400, Ostend, Belgium
| | - Jana Asselman
- Ghent University, Laboratory of Environmental Toxicology and Aquatic Ecology, Faculty of Bioscience Engineering, 9000, Ghent, Belgium; Blue Growth Research Lab, Ghent University, Bluebridge, Wetenschapspark 1, 8400, Ostend, Belgium
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6
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Corzo FL, Traverso L, Sterkel M, Benavente A, Ajmat MT, Ons S. Plodia interpunctella (Lepidoptera: Pyralidae): Intoxication with essential oils isolated from Lippia turbinata (Griseb.) and analysis of neuropeptides and neuropeptide receptors, putative targets for pest control. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 104:e21684. [PMID: 32329117 DOI: 10.1002/arch.21684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
The Indian meal moth Plodia interpunctella is a pest of stored products worldwide. Plant-derived essential oils with insecticidal activity could be safe products to control this species. The scarce information about the mode of action of most plant-derived products limits their use for the control of insect pests. Here, we demonstrate that an essential oil distilled from Lippia turbinata ("poleo") has insecticidal activity on P. interpunctella larvae. Furthermore, we performed a comprehensive characterization of P. interpunctella neuroendocrine system, in comparison with other lepidopteran species.
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Affiliation(s)
- Fernando Livio Corzo
- Instituto de Ambiente de Montaña y Regiones Áridas Universidad Nacional de Chilecito (IAMRA-UNdeC), La Rioja, Argentina
| | - Lucila Traverso
- Laboratorio de Neurobiología de Insectos, Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata, Argentina
| | - Marcos Sterkel
- Laboratorio de Neurobiología de Insectos, Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata, Argentina
| | - Alba Benavente
- Instituto de Ambiente de Montaña y Regiones Áridas Universidad Nacional de Chilecito (IAMRA-UNdeC), La Rioja, Argentina
| | - María Teresa Ajmat
- Instituto de Ambiente de Montaña y Regiones Áridas Universidad Nacional de Chilecito (IAMRA-UNdeC), La Rioja, Argentina
| | - Sheila Ons
- Laboratorio de Neurobiología de Insectos, Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, La Plata, Argentina
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7
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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Yang F, Li X, Li S, Xiang J, Li F. A novel cuticle protein involved in WSSV infection to the Pacific white shrimp Litopenaeus vannamei. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 102:103491. [PMID: 31494218 DOI: 10.1016/j.dci.2019.103491] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
As the most productive crustacean species in aquaculture, Litopenaeus vannamei is seriously threatened by white spot syndrome virus (WSSV), which has caused huge economic damage in the past decades. Shrimp cuticle proteins are the important components in the frontier target tissues, including cuticle and the chitinous lining of the digestive tract. In present study, a novel cuticle protein gene, named LvCPAP1, was isolated and demonstrated to play an important role in WSSV infection. The deduced amino acid sequence of LvCPAP1 contained a signal peptide and a conserved chitin-binding domain type 2 (ChBD2). Tissue distribution analysis revealed that LvCPAP1 was predominantly expressed in epidermis and stomach. The transcription levels of LvCPAP1 in epidermis and stomach were significantly regulated upon WSSV challenge. DsRNA silencing of LvCPAP1 decreased the in vivo WSSV copy numbers and the death rate of shrimp after WSSV infection, indicating that LvCPAP1 might facilitate WSSV invasion. In addition, the interaction between LvCPAP1 and the major envelop protein VP24 of WSSV was revealed by yeast two-hybrid system and further confirmed by dot blot and pull-down assays. The present study implied that cuticle protein LvCPAP1 might favor the entry process of WSSV, which provided new clues for understanding the role of cuticle proteins during virus infection.
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Affiliation(s)
- Feifei Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xuechun Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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Sigle LT, McGraw EA. Expanding the canon: Non-classical mosquito genes at the interface of arboviral infection. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 109:72-80. [PMID: 30970277 DOI: 10.1016/j.ibmb.2019.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/10/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Mosquito transmitted viruses cause significant morbidity and mortality in human populations. Despite the use of insecticides and other measures of vector control, arboviral diseases are on the rise. One potential solution for limiting disease transmission to humans is to render mosquitoes refractory to viral infection through genetic modification. Substantial research effort in Drosophila, Aedes and Anopheles has helped to define the major innate immune pathways, including Toll, IMD, Jak/Stat and RNAi, however we still have an incomplete picture of the mosquito antiviral response. Transcriptional profiles of virus-infected insects reveal a much wider range of pathways activated by the process of infection. Within these lists of genes are unexplored mosquito candidates of viral defense. Wolbachia species are endosymbiotic bacteria that naturally limit arboviral infection in mosquitoes. Our understanding of the Wolbachia-mediated viral blocking mechanism is poor, but it does not appear to operate via the classical immune pathways. Herein, we reviewed the transcriptomic response of mosquitoes to multiple viral species and put forth consensus gene types/families outside the immune canon whose expression responds to infection, including cytoskeleton and cellular trafficking, the heat shock response, cytochromes P450, cell proliferation, chitin and small RNAs. We then examine emerging evidence for their functional role in viral resistance in diverse insect and mammalian hosts and their potential role in Wolbachia-mediated viral blocking. These candidate gene families offer novel avenues for research into the nature of insect viral defense.
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Affiliation(s)
- Leah T Sigle
- Center for Infectious Disease Dynamics, Department of Entomology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Elizabeth A McGraw
- Center for Infectious Disease Dynamics, Department of Entomology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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10
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Sackton TB. Comparative genomics and transcriptomics of host-pathogen interactions in insects: evolutionary insights and future directions. CURRENT OPINION IN INSECT SCIENCE 2019; 31:106-113. [PMID: 31109663 DOI: 10.1016/j.cois.2018.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 12/21/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Classical evolutionary studies of protein-coding genes have established that genes in the canonical immune system are often among the most rapidly evolving within and between species. As more genomes and transcriptomes across insects are sequenced, it is becoming clear that duplications and losses of immune genes are also a likely consequence of host-pathogen interactions. Furthermore, particular species respond to diverse pathogenic challenges with a wide range of challenge-specific responses that are still poorly understood. Transcriptional studies, using RNA-seq to characterize the infection-regulated transcriptome of diverse insects, are crucial for additional progress in understanding the ecology and evolution of the full complexity of the host response.
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Affiliation(s)
- Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, United States.
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11
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Rotenberg D, Whitfield AE. Molecular interactions between tospoviruses and thrips vectors. Curr Opin Virol 2018; 33:191-197. [PMID: 30500681 DOI: 10.1016/j.coviro.2018.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023]
Abstract
Thrips-transmitted tospoviruses are an emerging and re-emerging threat to crop production worldwide. Tospoviruses are transstadially transmitted from larval to pupal stages of development, with adults serving as the primary inoculators of plants. A unique feature of the transmission cycle is that adults-while they can acquire virus from plants directly-are competent as vectors only if they acquire virus as larvae. Thrips vectors also serve as hosts for the virus, supporting its replication in midgut tissues and salivary glands. There is a tight link between thrips development and virus dissemination in the insect, and recent transcriptome studies point to stage-specific responses that coincide with localization of the virus in the insect body. Transcriptome sequencing of thrips vectors is leading to identification of virus-responsive thrips genes and possibly new targets to disrupt the virus transmission cycle. Accumulation of thrips-omics resources and advancements in functional biology tools will propel new and exciting molecular studies of thrips-tospoviruses interactions.
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Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
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12
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Palmer WH, Medd NC, Beard PM, Obbard DJ. Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses. PLoS Pathog 2018; 14:e1007050. [PMID: 29864164 PMCID: PMC6002114 DOI: 10.1371/journal.ppat.1007050] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 06/14/2018] [Accepted: 04/20/2018] [Indexed: 12/15/2022] Open
Abstract
Drosophila melanogaster has played a key role in our understanding of invertebrate immunity. However, both functional and evolutionary studies of host-virus interaction in Drosophila have been limited by a dearth of native virus isolates. In particular, despite a long history of virus research, DNA viruses of D. melanogaster have only recently been described, and none have been available for experimental study. Here we report the isolation and comprehensive characterisation of Kallithea virus, a large double-stranded DNA virus, and the first DNA virus to have been reported from wild populations of D. melanogaster. We find that Kallithea virus infection is costly for adult flies, reaching high titres in both sexes and disproportionately reducing survival in males, and movement and late fecundity in females. Using the Drosophila Genetic Reference Panel, we quantify host genetic variance for virus-induced mortality and viral titre and identify candidate host genes that may underlie this variation, including Cdc42-interacting protein 4. Using full transcriptome sequencing of infected males and females, we examine the transcriptional response of flies to Kallithea virus infection and describe differential regulation of virus-responsive genes. This work establishes Kallithea virus as a new tractable model to study the natural interaction between D. melanogaster and DNA viruses, and we hope it will serve as a basis for future studies of immune responses to DNA viruses in insects.
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Affiliation(s)
- William H Palmer
- Institute of Evolutionary Biology University of Edinburgh, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Nathan C Medd
- Institute of Evolutionary Biology University of Edinburgh, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Philippa M Beard
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Darren J Obbard
- Institute of Evolutionary Biology University of Edinburgh, Charlotte Auerbach Road, Edinburgh, United Kingdom
- Centre for Infection, Evolution and Immunity, University of Edinburgh, Edinburgh, United Kingdom
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13
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Zheng JC, Sun SL, Yue XR, Liu TX, Jing X. Phylogeny and evolution of the cholesterol transporter NPC1 in insects. JOURNAL OF INSECT PHYSIOLOGY 2018; 107:157-166. [PMID: 29649482 DOI: 10.1016/j.jinsphys.2018.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/08/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Sterols are essential nutrients for eukaryotes. Insects are obligate sterol auxotrophs and must acquire this key nutrient from their diets. The digestive tract is the organ for absorbing nutrients as well as sterols from food. In mice, the Niemann-Pick type C1 Like 1 (NPC1L1) gene is highly expressed in the intestine and is critical for cholesterol absorption. In contrast, the molecular mechanisms for the absorption of dietary sterols in insects have not been well studied. We annotated NPC1 genes in 39 insects from 10 orders using available genomic and transcriptomic information and inferred phylogenetic relationships. Insect NPC1 genes were grouped into two sister-clades, NPC1a and NPC1b, suggesting a likely duplication in the ancestor of insects. The former exhibited weaker gut-biased expression or a complete lack of tissue-biased expression, depending on the species, while the latter was highly enriched in the gut of three lepidopteran species. This result is similar to previous findings in Drosophila melanogaster. In insects, NPC1a accumulated non-synonymous substitutions at a lower rate than NPC1b. This pattern was consistent across orders, indicating that NPC1a evolved under stronger molecular constraint than NPC1b.
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Affiliation(s)
- Jin-Cheng Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shao-Lei Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Rong Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong-Xian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiangfeng Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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14
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Jia X, Zhang X, Liu H, Wang R, Zhang T. Identification of chemosensory genes from the antennal transcriptome of Indian meal moth Plodia interpunctella. PLoS One 2018; 13:e0189889. [PMID: 29304134 PMCID: PMC5755773 DOI: 10.1371/journal.pone.0189889] [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: 09/19/2017] [Accepted: 12/04/2017] [Indexed: 11/30/2022] Open
Abstract
Olfaction plays an indispensable role in mediating insect behavior, such as locating host plants, mating partners, and avoidance of toxins and predators. Olfactory-related proteins are required for olfactory perception of insects. However, very few olfactory-related genes have been reported in Plodia interpunctella up to now. In the present study, we sequenced the antennae transcriptome of P. interpunctella using the next-generation sequencing technology, and identified 117 candidate olfactory-related genes, including 29 odorant-binding proteins (OBPs), 15 chemosensory proteins (CSPs), three sensory neuron membrane proteins (SNMPs), 47 odorant receptors (ORs), 14 ionotropic receptors (IRs) and nine gustatory receptors (GRs). Further analysis of qRT-PCR revealed that nine OBPs, three CSPs, two SNMPs, nine ORs and two GRs were specifically expressed in the male antennae, whereas eight OBPs, six CSPs, one SNMP, 16 ORs, two GRs and seven IRs significantly expressed in the female antennae. Taken together, our results provided useful information for further functional studies on insect genes related to recognition of pheromone and odorant, which might be meaningful targets for pest management.
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Affiliation(s)
- Xiaojian Jia
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences/Integrated Pest Management Center of Hebei Province/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, P. R. China
| | - Xiaofang Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences/Integrated Pest Management Center of Hebei Province/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, P. R. China
| | - Hongmin Liu
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, P. R. China
| | - Rongyan Wang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences/Integrated Pest Management Center of Hebei Province/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, P. R. China
| | - Tao Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences/Integrated Pest Management Center of Hebei Province/Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, P. R. China
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15
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Tang PA, Wu HJ, Xue H, Ju XR, Song W, Zhang QL, Yuan ML. Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages. Gene 2017; 622:29-41. [PMID: 28412460 DOI: 10.1016/j.gene.2017.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/01/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest.
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Affiliation(s)
- Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China.
| | - Hai-Jing Wu
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Hao Xue
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Xing-Rong Ju
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Wei Song
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Qi-Lin Zhang
- Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
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16
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Thrips developmental stage-specific transcriptome response to tomato spotted wilt virus during the virus infection cycle in Frankliniella occidentalis, the primary vector. Virology 2016; 500:226-237. [PMID: 27835811 DOI: 10.1016/j.virol.2016.10.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/07/2016] [Accepted: 10/09/2016] [Indexed: 12/25/2022]
Abstract
Tomato spotted wilt virus (TSWV) is transmitted by Frankliniella occidentalis in a circulative-propagative manner. Little is known about thrips vector response to TSWV during the infection process from larval acquisition to adult inoculation of plants. Whole-body transcriptome response to virus infection was determined for first-instar larval, pre-pupal and adult thrips using RNA-Seq. TSWV responsive genes were identified using preliminary sequence of a draft genome of F. occidentalis as a reference and three developmental-stage transcriptomes were assembled. Processes and functions associated with host defense, insect cuticle structure and development, metabolism and transport were perturbed by TSWV infection as inferred by ontologies of responsive genes. The repertoire of genes responsive to TSWV varied between developmental stages, possibly reflecting the link between thrips development and the virus dissemination route in the vector. This study provides the foundation for exploration of tissue-specific expression in response to TSWV and functional analysis of thrips gene function.
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17
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Transcriptome Analysis of the Midgut of the Chinese Oak Silkworm Antheraea pernyi Infected with Antheraea pernyi Nucleopolyhedrovirus. PLoS One 2016; 11:e0165959. [PMID: 27820844 PMCID: PMC5098726 DOI: 10.1371/journal.pone.0165959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022] Open
Abstract
The Antheraea pernyi nucleopolyhedrovirus (ApNPV) is an exclusive pathogen of A. pernyi. The intense interactions between ApNPV and A. pernyi cause a series of physiological and pathological changes to A. pernyi. However, no detailed report exists regarding the molecular mechanisms underlying the interactions between ApNPV and A. pernyi. In this study, four cDNA libraries of the A. pernyi midgut, including two ApNPV-infected groups and two control groups, were constructed for transcriptomic analysis to provide new clues regarding the molecular mechanisms that underlie these interactions. The transcriptome of the A. pernyi midgut was de novo assembled using the Trinity platform because of the lack of a genome resource for A. pernyi. Compared with the controls, a total of 5,172 differentially expressed genes (DEGs) were identified, including 2,183 up-regulated and 2,989 down-regulated candidates, of which 2,965 and 911 DEGs were classified into different GO categories and KEGG pathways, respectively. The DEGs involved in A. pernyi innate immunity were classified into several categories, including heat-shock proteins, apoptosis-related proteins, serpins, serine proteases and cytochrome P450s. Our results suggested that these genes were related to the immune response of the A. pernyi midgut to ApNPV infection via their essential roles in regulating a variety of physiological processes. Our results may serve as a basis for future research not only on the molecular mechanisms of ApNPV invasion but also on the anti-ApNPV mechanism of A. pernyi.
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18
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Nguyen Q, Tb Tran T, Chan LC, Nielsen LK, Reid S. In vitro production of baculoviruses: identifying host and virus genes associated with high productivity. Appl Microbiol Biotechnol 2016; 100:9239-9253. [PMID: 27613424 DOI: 10.1007/s00253-016-7774-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 01/22/2023]
Abstract
Baculoviruses are recognized as viral workhorses of biotechnology, being used for production of vaccines, complex recombinant proteins, gene delivery vectors' and safe biological pesticides. Improving production yields and understanding the interactions of the virus and its host cell are important aspects of ensuring baculovirus-based processes are commercially competitive. This study aims at potential optimization of host cells used in in vitro virus production by systemically investigating changes in host gene expression in response to virus replication and transcription inside host cells. The study focuses on in vitro interactions of the Helicoverpa armigera virus with Helicoverpa zea insect cells. We used 22 genome-wide microarrays to simultaneously measure both virus and host genes in infected cells in multiple batch suspension cultures, representing high- and low-producing infection conditions. Among 661 differentially expressed genes, we identified a core set of 59 host genes consistently overexpressed post infection, with strong overrepresentation of genes involved in retrotransposition, protein processing in the endoplasmic reticulum, and ubiquitin-mediated proteolysis. Applying a whole genome correlation network analysis to link gene expression to productivity, we revealed 18 key genes significantly associated to virus yield. In addition, this study is among the first to perform a genome-wide expression study for a major baculovirus group II strain, the H. armigera virus, extending current understanding of baculovirus-insect interactions, which mainly focuses on group I viruses.
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Affiliation(s)
- Quan Nguyen
- Livestock Genomics, CSIRO (The Commonwealth Scientific and Industrial Research Organisation) Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Trinh Tb Tran
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Leslie Cl Chan
- Patheon Biologics, 37 Kent street, Brisbane, QLD, 4102, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Steven Reid
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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19
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Harrison RL, Rowley DL, Funk CJ. The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene. PLoS One 2016; 11:e0160389. [PMID: 27472489 PMCID: PMC4966970 DOI: 10.1371/journal.pone.0160389] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
The Indianmeal moth, Plodia interpunctella (Lepidoptera: Pyralidae), is a common pest of stored goods with a worldwide distribution. The complete genome sequence for a larval pathogen of this moth, the baculovirus Plodia interpunctella granulovirus (PiGV), was determined by next-generation sequencing. The PiGV genome was found to be 112, 536 bp in length with a 44.2% G+C nucleotide distribution. A total of 123 open reading frames (ORFs) and seven homologous regions (hrs) were identified and annotated. Phylogenetic inference using concatenated alignments of 36 baculovirus core genes placed PiGV in the “b” clade of viruses from genus Betabaculovirus with a branch length suggesting that PiGV represents a distinct betabaculovirus species. In addition to the baculovirus core genes and orthologues of other genes found in other betabaculovirus genomes, the PiGV genome sequence contained orthologues of the bidensovirus NS3 gene, as well as ORFs that occur in alphabaculoviruses but not betabaculoviruses. While PiGV contained an orthologue of inhibitor of apoptosis-5 (iap-5), an orthologue of inhibitor of apoptosis-3 (iap-3) was not present. Instead, the PiGV sequence contained an ORF (PiGV ORF81) encoding an IAP homologue with sequence similarity to insect cellular IAPs, but not to viral IAPs. Phylogenetic analysis of baculovirus and insect IAP amino acid sequences suggested that the baculovirus IAP-3 genes and the PiGV ORF81 IAP homologue represent different lineages arising from more than one acquisition event. The presence of genes from other sources in the PiGV genome highlights the extent to which baculovirus gene content is shaped by horizontal gene transfer.
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Affiliation(s)
- Robert L. Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
| | - Daniel L. Rowley
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - C. Joel Funk
- Department of Biology, John Brown University, Siloam Springs, Arkansas, United States of America
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Moreton J, Izquierdo A, Emes RD. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. Front Genet 2016; 6:361. [PMID: 26793234 PMCID: PMC4707302 DOI: 10.3389/fgene.2015.00361] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 12/19/2015] [Indexed: 11/13/2022] Open
Abstract
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems?
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Affiliation(s)
- Joanna Moreton
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
| | - Richard D. Emes
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of NottinghamLeicestershire, UK
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