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Sun Y, Yang P, Jin H, Liu H, Zhou H, Qiu L, Lin Y, Ma W. Knockdown of the aminopeptidase N genes decreases susceptibility of Chilo suppressalis larvae to Cry1Ab/Cry1Ac and Cry1Ca. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 162:36-42. [PMID: 31836052 DOI: 10.1016/j.pestbp.2019.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/09/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Bacillus thuringiensis (Bt) insecticide is currently the most widely used bioinsecticide. Bt expressing cry genes are some of the most successful foreign-genome-inserting genes used in transgenic insect-resistant crop development. Cry toxins are resistant to lepidopteran pests, such as Chilo suppressalis, a major insect pest of rice worldwide. Since Cry toxins exert their activity by binding to specific receptors in the midgut of target insects, identification of functional Cry toxin receptors in the midgut of C. suppressalis larvae is crucial to evaluate potential resistance mechanisms and develop effective strategies for inhibiting insect resistance. In this study, we isolated two aminopeptidase N genes (APN6 and APN8) from C. suppressalis and determined that they were expressed in the foregut. APN6 was highly expressed at the fourth instar, and APN8 was highly expressed in adult and pupa. Knockdown of CsAPN6 and CsAPN8 by RNA interference resulted in significantly decreased susceptibility of larvae to Bt rice varieties TT51 (expressing cry1Ac/cry1Ab fusion genes) and T1C-19 (expressing cry1Ca), but not T2A-1 (expressing cry2Aa). These findings suggest that both APN6 and APN8 are involved in the toxicity of Cry1Ac/Cry1Ab and Cry1Ca toxins.
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Affiliation(s)
- Yajie Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Pan Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Huihui Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hui Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lin Qiu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan 430070, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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52
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Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
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Affiliation(s)
- F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - X Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - C Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Y Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Z Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - J R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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53
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Shi M, Wang Z, Ye X, Xie H, Li F, Hu X, Wang Z, Yin C, Zhou Y, Gu Q, Zou J, Zhan L, Yao Y, Yang J, Wei S, Hu R, Guo D, Zhu J, Wang Y, Huang J, Pennacchio F, Strand MR, Chen X. The genomes of two parasitic wasps that parasitize the diamondback moth. BMC Genomics 2019; 20:893. [PMID: 31752718 PMCID: PMC6873472 DOI: 10.1186/s12864-019-6266-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 11/05/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Parasitic insects are well-known biological control agents for arthropod pests worldwide. They are capable of regulating their host's physiology, development and behaviour. However, many of the molecular mechanisms involved in host-parasitoid interaction remain unknown. RESULTS We sequenced the genomes of two parasitic wasps (Cotesia vestalis, and Diadromus collaris) that parasitize the diamondback moth Plutella xylostella using Illumina and Pacbio sequencing platforms. Genome assembly using SOAPdenovo produced a 178 Mb draft genome for C. vestalis and a 399 Mb draft genome for D. collaris. A total set that contained 11,278 and 15,328 protein-coding genes for C. vestalis and D. collaris, respectively, were predicted using evidence (homology-based and transcriptome-based) and de novo prediction methodology. Phylogenetic analysis showed that the braconid C. vestalis and the ichneumonid D. collaris diverged approximately 124 million years ago. These two wasps exhibit gene gains and losses that in some cases reflect their shared life history as parasitic wasps and in other cases are unique to particular species. Gene families with functions in development, nutrient acquisition from hosts, and metabolism have expanded in each wasp species, while genes required for biosynthesis of some amino acids and steroids have been lost, since these nutrients can be directly obtained from the host. Both wasp species encode a relative higher number of neprilysins (NEPs) thus far reported in arthropod genomes while several genes encoding immune-related proteins and detoxification enzymes were lost in both wasp genomes. CONCLUSIONS We present the annotated genome sequence of two parasitic wasps C. vestalis and D. collaris, which parasitize a common host, the diamondback moth, P. xylostella. These data will provide a fundamental source for studying the mechanism of host control and will be used in parasitoid comparative genomics to study the origin and diversification of the parasitic lifestyle.
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Affiliation(s)
- Min Shi
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Zhizhi Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Xiqian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | | | - Fei Li
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoxiao Hu
- BGI-Tech, BGI-Shenzhen, Shenzhen, 518083, China
- Xingzhi College, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
| | - Zehua Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Chuanlin Yin
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Yuenan Zhou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Qijuan Gu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Jiani Zou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Leqing Zhan
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Yuan Yao
- School of Physical Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Jian Yang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Shujun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Rongmin Hu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Dianhao Guo
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China
| | - Jiangyan Zhu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | - Yanping Wang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | - Jianhua Huang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China.
| | - Francesco Pennacchio
- Dipartimento di Agraria, Laboratorio di Entomologia "E. Tremblay", Università di Napoli "Federico II", Via Università 100, 80055, Portici, NA, Italy
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, 310058, China.
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
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54
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Tian R, Zhang C, Huang Y, Guo X, Chen M. A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data. Genes (Basel) 2019; 10:E917. [PMID: 31717904 PMCID: PMC6895799 DOI: 10.3390/genes10110917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022] Open
Abstract
Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.
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Affiliation(s)
| | | | | | | | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China; (R.T.); (C.Z.); (Y.H.); (X.G.)
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55
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Finet C, Slavik K, Pu J, Carroll SB, Chung H. Birth-and-Death Evolution of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Diversification of Cuticular Hydrocarbon Synthesis in Drosophila. Genome Biol Evol 2019; 11:1541-1551. [PMID: 31076758 PMCID: PMC6546124 DOI: 10.1093/gbe/evz094] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
The birth-and-death evolutionary model proposes that some members of a multigene family are phylogenetically stable and persist as a single copy over time, whereas other members are phylogenetically unstable and undergo frequent duplication and loss. Functional studies suggest that stable genes are likely to encode essential functions, whereas rapidly evolving genes reflect phenotypic differences in traits that diverge rapidly among species. One such class of rapidly diverging traits are insect cuticular hydrocarbons (CHCs), which play dual roles in chemical communications as short-range recognition pheromones as well as protecting the insect from desiccation. Insect CHCs diverge rapidly between related species leading to ecological adaptation and/or reproductive isolation. Because the CHC and essential fatty acid biosynthetic pathways share common genes, we hypothesized that genes involved in the synthesis of CHCs would be evolutionary unstable, whereas those involved in fatty acid-associated essential functions would be evolutionary stable. To test this hypothesis, we investigated the evolutionary history of the fatty acyl-CoA reductases (FARs) gene family that encodes enzymes in CHC synthesis. We compiled a unique data set of 200 FAR proteins across 12 Drosophila species. We uncovered a broad diversity in FAR content which is generated by gene duplications, subsequent gene losses, and alternative splicing. We also show that FARs expressed in oenocytes and presumably involved in CHC synthesis are more unstable than FARs from other tissues. Taken together, our study provides empirical evidence that a comparative approach investigating the birth-and-death evolution of gene families can identify candidate genes involved in rapidly diverging traits between species.
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Affiliation(s)
- Cédric Finet
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, France
| | - Kailey Slavik
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison.,PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Jian Pu
- Department of Entomology, Michigan State University
| | - Sean B Carroll
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison.,Department of Biology, University of Maryland, College Park, MD
| | - Henry Chung
- Department of Entomology, Michigan State University.,Ecology, Evolutionary Biology and Behavior, Michigan State University
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56
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Identification of candidate ATP-binding cassette transporter gene family members in Diaphorina citri (Hemiptera: Psyllidae) via adult tissues transcriptome analysis. Sci Rep 2019; 9:15842. [PMID: 31676883 PMCID: PMC6825165 DOI: 10.1038/s41598-019-52402-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette (ABC) transporters exist in all living organisms and play major roles in various biological functions by transporting a wide variety of substrates across membranes. The functions of ABC transporters in drug resistance have been extensively studied in vertebrates; however, they are rarely characterized in agricultural pests. The Asian citrus psyllid, Diaphorina citri, is one of the most damaging pests of the Citrus genus because of its transmission of Huanglongbing, also known as Yellow Dragon disease. In this study, the next-generation sequencing technique was applied to research the ABC transporters of D. citri. Fifty-three ABC transporter genes were found in the RNA-Seq data, and among these ABC transporters, 4, 4, 5, 2, 1, 4, 18 and 15 ABC proteins belonged to the ABCA-ABCH subfamilies, respectively. Different expression profiles of 52 genes between imidacloprid-resistant and imidacloprid-susceptible strains were studied by qRT-PCR; 5 ABCGs and 4 ABCHs were significantly upregulated in the imidacloprid-resistant strain. In addition, five of the nine upregulated genes were widely expressed in adult tissues in spatial expression analysis. The results suggest that these genes may play key roles in this phenotype. In general, this study contributed to our current understanding of D. citri resistance to insecticides.
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57
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Omar MAA, Ao Y, Li M, He K, Xu L, Tong H, Jiang M, Li F. The functional difference of eight chitinase genes between male and female of the cotton mealybug, Phenacoccus solenopsis. INSECT MOLECULAR BIOLOGY 2019; 28:550-567. [PMID: 30739379 DOI: 10.1111/imb.12572] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) is a polyphagous insect that attacks tens of plant and causes substantial economic loss. Insect chitinases are required to remove the old cuticle to allow for continued growth and development. Though insect chitinases have been well studied in tens of insects, their functions in mealybug are still not addressed. Here, we sequenced the transcriptomes of adult males and females, from which eight chitinase genes were identified. We then used the method of rapid amplification of cDNA ends to amplify their full length. Phylogenetic analysis indicated that these genes clustered into five subgroups. Among which, group II PsCht2 had the longest transcript and was highly expressed at second instar nymph. PsCht10, PsCht3-3 and PsIDGF were highly expressed in the adult females, whereas PsCht4 and PsCht4-1 were significantly expressed at the male pupa and adult male. Next, we knocked down all eight chitinase genes by feeding the double-stranded RNA. Knockdown of PsCht4 or PsCht4-1 led to the failure of moult and, silencing PsCht5 resulted in pupation defect, while silencing PsCht10 led to small body size, suggesting these genes have essential roles in development and can be used as a potential target for pest control.
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Affiliation(s)
- Mohamed A A Omar
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
- Department of Plant Protection, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Y Ao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - L Xu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - H Tong
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - M Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, Hangzhou, China
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58
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He K, Xiao H, Sun Y, Situ G, Xi Y, Li F. microRNA-14 as an efficient suppressor to switch off ecdysone production after ecdysis in insects. RNA Biol 2019; 16:1313-1325. [PMID: 31184522 DOI: 10.1080/15476286.2019.1629768] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The precise increase and decrease of hormone ecdysone are critical for accurate development in insects. Most previous works focus on transcriptional activation of ecdysone production; however, little is known about the mechanism of switching off ecdysone biosynthesis after ecdysis. Here, we showed that the precursor microRNA-14 (pre-miR-14) encodes two mature miRNAs in silkworm; both of these two mature miRNAs regulate various genes in the ecdysone-signalling pathway. Bmo-miR-14-5p targets on nine genes whereas Bmo-miR-14-3p targets on two genes in the same pathway. These two mature miRNAs increased immediately after the ecdysis, efficiently suppressing the 20-hydroxyecdysone (20E) biosynthesis, the upstream regulation, and the downstream response genes. Knocking down either of two mature miRNAs or both of them delays moult development, impairing development synchrony in antagomir-treated groups. In addition, overexpressing Bmo-miR-14-5p but not Bmo-miR-14-3p significantly affected the 20E titer and increased the moulting time variation, suggesting that Bmo-miR-14-5p, though it is less abundant, has more potent effects in development regulation than Bmo-miR-14-3p. In summary, we present evidence that a pre-miRNA encodes two mature miRNAs targeting on the same pathway, which significantly improves miRNA regulation efficiencies to programmatically switch off ecdysone biosynthesis.
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Affiliation(s)
- Kang He
- a Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou , China
| | - Huamei Xiao
- b College of Life Sciences and Resource Environment, Yichun University , Yichun , China.,c Department of Entomology, Nanjing Agricultural University , Nanjing , China
| | - Yang Sun
- c Department of Entomology, Nanjing Agricultural University , Nanjing , China.,d Institute of Plant Protection, Jiangxi Academy of Agricultural Science , Nanchang , China
| | - Gongming Situ
- c Department of Entomology, Nanjing Agricultural University , Nanjing , China
| | - Yu Xi
- e Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen , China
| | - Fei Li
- a Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University , Hangzhou , China
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59
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Meinzer F, Dobler S, Donath A, Lohr JN. Robust reference gene design and validation for expression studies in the large milkweed bug, Oncopeltus fasciatus, upon cardiac glycoside stress. Gene 2019; 710:66-75. [PMID: 31108166 DOI: 10.1016/j.gene.2019.05.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 04/06/2019] [Accepted: 05/13/2019] [Indexed: 11/18/2022]
Abstract
Despite its history as a developmental and evolutionary model organism, gene expression analysis in the large milkweed bug, Oncopeltus fasciatus, has rarely been explored using quantitative real-time PCR. The strength of this method depends greatly on the endogenous controls used for normalization, which are lacking for the milkweed bug system. Here, to fill in this gap in our knowledge, we validated the stability of a set of ten candidate reference genes identified from the O. fasciatus transcriptome, and did so upon exposure to a dietary toxin, a cardiac glycoside, and across four different exposure periods. To increase robustness against gDNA contaminants, genome resources were used to design intron-bridging primers. A comprehensive stability validation by the Bestkeeper, Normfinder, geNorm and comparative ΔCt methods identified ef1a and tubulin as the most stable genes across treatments and time points, whereas 18S rRNA was the most unstable. However, accounting for the temporal scale indicated that time point confined normalizers might enable higher quantification accuracy for treatment comparison. Overall this study demonstrates: (i) a robust RT-qPCR primer design approach is possible for non-model organisms where genome annotation is often incomplete, and (ii) the importance of detailed reference gene stability exploration in multifactorial experimental designs.
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Affiliation(s)
- Fee Meinzer
- Molekulare Evolutionsbiologie, Institut für Zoologie, Universität Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany.
| | - Susanne Dobler
- Molekulare Evolutionsbiologie, Institut für Zoologie, Universität Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Alexander Donath
- Zentrum für Molekulare Biodiversitätsforschung, Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Jennifer N Lohr
- Molekulare Evolutionsbiologie, Institut für Zoologie, Universität Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
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60
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Belghit I, Lock EJ, Fumière O, Lecrenier MC, Renard P, Dieu M, Berntssen MHG, Palmblad M, Rasinger JD. Species-Specific Discrimination of Insect Meals for Aquafeeds by Direct Comparison of Tandem Mass Spectra. Animals (Basel) 2019; 9:E222. [PMID: 31067722 PMCID: PMC6562778 DOI: 10.3390/ani9050222] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 01/07/2023] Open
Abstract
Insect protein has the potential to become a sustainable feed ingredient for the rapidly growing aquaculture industry. In the European Union, insect derived protein is placed under the same legislation as processed animal proteins (PAP). It is therefore of interest to develop methods for regulatory use, which unambiguously identify the species origin of insect-based ingredients. We performed (i) total protein quantification of insect samples using the traditional nitrogen-to-protein conversion factor of 6.25 and the sum of anhydrous amino acids, (ii) quantitative amino acid profiling and (iii) high-throughput tandem mass spectrometry to describe and differentiate 18 different commercial-grade insect meal samples derived from Hermetia illucens (8), Tenebrio molitor (5), Alphitobius diaperinus (3) and Acheta domesticus (2). In addition, we investigated and compared different protein extraction and digestion protocols for proteomic analysis. We found that irrespective of sample preparation, shotgun proteomics in combination with direct spectral comparison were able to differentiate insect meal according to their taxonomic classification. The insect specific spectral libraries created in the present work can in future be used to develop more sensitive targeted methods of insect PAP identification and quantification in commercial feed mixtures.
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Affiliation(s)
- Ikram Belghit
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway.
| | - Erik-Jan Lock
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway.
| | - Olivier Fumière
- Centre Wallon de Recherches agronomiques (CRA-W), 5030 Gembloux, Belgium.
| | | | - Patricia Renard
- University of Namur, rue de Bruxelles 61, B-5000 Namur, Belgium.
| | - Marc Dieu
- University of Namur, rue de Bruxelles 61, B-5000 Namur, Belgium.
- University of Namur, mass spectrometry facility (MaSUN), rue de Bruxelles 61, B-5000 Namur, Belgium.
| | - Marc H G Berntssen
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway.
| | - Magnus Palmblad
- Leids Universitair Medisch Centrum, 2316 Leiden, The Netherlands.
| | - Josef D Rasinger
- Institute of Marine Research, P.O. Box 1870 Nordnes, 5817 Bergen, Norway.
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Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
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Salcedo-Porras N, Guarneri A, Oliveira PL, Lowenberger C. Rhodnius prolixus: Identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria. PLoS One 2019; 14:e0214794. [PMID: 30943246 PMCID: PMC6447187 DOI: 10.1371/journal.pone.0214794] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/20/2019] [Indexed: 12/16/2022] Open
Abstract
The innate immune system in insects is regulated by specific signalling pathways. Most immune related pathways were identified and characterized in holometabolous insects such as Drosophila melanogaster, and it was assumed they would be highly conserved in all insects. The hemimetabolous insect, Rhodnius prolixus, has served as a model to study basic insect physiology, but also is a major vector of the human parasite, Trypanosoma cruzi, that causes 10,000 deaths annually. The publication of the R. prolixus genome revealed that one of the main immune pathways, the Immune-deficiency pathway (IMD), was incomplete and probably non-functional, an observation shared with other hemimetabolous insects including the pea aphid (Acyrthosiphon pisum) and the bedbug (Cimex lectularius). It was proposed that the IMD pathway is inactive in R. prolixus as an adaptation to prevent eliminating beneficial symbiont gut bacteria. We used bioinformatic analyses based on reciprocal BLAST and HMM-profile searches to find orthologs for most of the "missing" elements of the IMD pathway and provide data that these are regulated in response to infection with Gram-negative bacteria. We used RNAi strategies to demonstrate the role of the IMD pathway in regulating the expression of specific antimicrobial peptides (AMPs) in the fat body of R. prolixus. The data indicate that the IMD pathway is present and active in R. prolixus, which opens up new avenues of research on R. prolixus-T. cruzi interactions.
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Affiliation(s)
- Nicolas Salcedo-Porras
- Centre for Cell Biology, Development, and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alessandra Guarneri
- Instituto René Rachou, Avenida Augusto de Lima, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro L. Oliveira
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, CCS, Ilha do Fundão, Rio de Janeiro, Brazil
| | - Carl Lowenberger
- Centre for Cell Biology, Development, and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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UDP-Glycosyltransferase Genes in the Striped Rice Stem Borer, Chilo suppressalis (Walker), and Their Contribution to Chlorantraniliprole Resistance. Int J Mol Sci 2019; 20:ijms20051064. [PMID: 30823656 PMCID: PMC6429375 DOI: 10.3390/ijms20051064] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 12/01/2022] Open
Abstract
Uridine diphosphate glycosyltransferases (UGTs) are multifunctional detoxification enzymes, which are involved in metabolizing various chemicals and contribute to the development of insecticide resistance. However, the possible roles of UGTs in chlorantraniliprole resistance in Chilo suppressalis have rarely been studied in detail. Based on genome data, 24 UGT genes in C. suppressalis belonging to 11 families were identified, which were designated by the UGT nomenclature committee. Synergism assay data suggested that UGTs are potentially involved in chlorantraniliprole resistance in C. suppressalis.CsUGT40AL1 and CsUGT33AG3 were significantly overexpressed in the chlorantraniliprole resistant strain (12.36- and 5.34-fold, respectively). The two UGTs were highly expressed in the larval Malpighian tubules, fat body, and midgut; however, expression was lowest in the head. Injection of individual dsRNAs reduced the expression of the two target genes (by 69.34% and 48.74%, respectively) and caused significant higher larval mortality (81.33% and 54.67%, respectively). Overexpression of CsUGT40AL1 and CsUGT33AG3 was potentially involved in chlorantraniliprole resistance in C. suppressalis, as confirmed by the RNAi assay. Our findings suggest that overexpression of UGTs may contribute to chlorantraniliprole resistance in C. suppressalis.
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Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int J Mol Sci 2019; 20:E1072. [PMID: 30832228 PMCID: PMC6429444 DOI: 10.3390/ijms20051072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/30/2022] Open
Abstract
Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
- Department of Entomology, China Agricultural University, Beijing 100193, China.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.
| | - Liming Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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Nardelli A, Vecchi M, Mandrioli M, Manicardi GC. The Evolutionary History and Functional Divergence of Trehalase ( treh) Genes in Insects. Front Physiol 2019; 10:62. [PMID: 30828300 PMCID: PMC6384254 DOI: 10.3389/fphys.2019.00062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/21/2019] [Indexed: 01/04/2023] Open
Abstract
Trehalases (treh) have been found in different organisms, such as bacteria, fungi, yeast, nematodes, insects, vertebrates, and plants. Their biochemical properties are extremely variable and not yet fully understood. Gene expression patterns have shown differences among insect species suggesting a potential functional diversification of trehalase enzymes during their evolution. A second gene family encoding for enzymes with hypothetical trehalase activity has been repeatedly annotated in insect genome as acid trehalases/acid trehalase-like (ath), but its functional role is still not clear. The currently available large amount of genomic data from many insect species may enable a better understanding of the evolutionary history, phylogenetic relationships and possible roles of trehalase encoding genes in this taxon. The aim of the present study is to infer the evolutionary history of trehalases and acid trehalase genes in insects and analyze the trehalase functional divergence during their evolution, combining phylogenetic and genomic synteny/colinearity analyses.
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Affiliation(s)
- Andrea Nardelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Vecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Sarmashghi S, Bohmann K, P. Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol 2019; 20:34. [PMID: 30760303 PMCID: PMC6374904 DOI: 10.1186/s13059-019-1632-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 01/16/2019] [Indexed: 01/10/2023] Open
Abstract
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.
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Affiliation(s)
- Shahab Sarmashghi
- Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093 CA USA
| | - Kristine Bohmann
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk UK
| | - M. Thomas P. Gilbert
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, Trondheim, 7491 Norway
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, 92093 CA USA
| | - Siavash Mirarab
- Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093 CA USA
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Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol 2019; 2:56. [PMID: 30775457 PMCID: PMC6368629 DOI: 10.1038/s42003-019-0306-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Benjamin Brandt
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Andres Veidenberg
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Markéta Luklová
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- Present Address: Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC—Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
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Tvedte ES, Logsdon JM, Forbes AA. Sex loss in insects: causes of asexuality and consequences for genomes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:77-83. [PMID: 31109677 DOI: 10.1016/j.cois.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/03/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.
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Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, United States
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69
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Wang XR, Wang C, Ban FX, Zhu DT, Liu SS, Wang XW. Genome-wide identification and characterization of HSP gene superfamily in whitefly (Bemisia tabaci) and expression profiling analysis under temperature stress. INSECT SCIENCE 2019; 26:44-57. [PMID: 28714602 DOI: 10.1111/1744-7917.12505] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 05/22/2017] [Accepted: 06/01/2017] [Indexed: 05/14/2023]
Abstract
Heat shock proteins (HSP) are essential molecular chaperones that play important roles in the stress stimulation of insects. Bemisia tabaci, a phloem feeder and invasive species, can cause extensive crop damage through direct feeding and transmission of plant viruses. Here we employed comprehensive genomics approaches to identity HSP superfamily members in the Middle East Asia Minor 1 whitefly genome. In total, we identified 26 Hsp genes, including three Hsp90, 17 Hsp70, one Hsp60 and five sHSP (small heat shock protein) genes. The HSP gene superfamily of whitefly is expanded compared with the other five insects surveyed here. The gene structures among the same families are relatively conserved. Meanwhile, the motif compositions and secondary structures of BtHsp proteins were predicted. In addition, quantitative polymerase chain reaction analysis showed that the expression patterns of BtHsp gene superfamily were diverse across different tissues of whiteflies. Most Hsp genes were induced or repressed by thermal stress (40°C) and cold treatment (4°C) in whitefly. Silencing the expression of BtHsp70-6 significantly decreased the survival rate of whitefly under 45°C. All the results showed the Hsps conferred thermo-tolerance or cold-tolerance to whiteflies that protect them from being affected by detrimental temperature conditions. Our observations highlighted the molecular evolutionary properties and the response mechanism to temperature assaults of Hsp genes in whitefly.
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Affiliation(s)
- Xin-Ru Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chao Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei-Xue Ban
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Dan-Tong Zhu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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70
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Da Lage JL, Thomas GWC, Bonneau M, Courtier-Orgogozo V. Evolution of salivary glue genes in Drosophila species. BMC Evol Biol 2019; 19:36. [PMID: 30696414 PMCID: PMC6352337 DOI: 10.1186/s12862-019-1364-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 11/23/2022] Open
Abstract
Background At the very end of the larval stage Drosophila expectorate a glue secreted by their salivary glands to attach themselves to a substrate while pupariating. The glue is a mixture of apparently unrelated proteins, some of which are highly glycosylated and possess internal repeats. Because species adhere to distinct substrates (i.e. leaves, wood, rotten fruits), glue genes are expected to evolve rapidly. Results We used available genome sequences and PCR-sequencing of regions of interest to investigate the glue genes in 20 Drosophila species. We discovered a new gene in addition to the seven glue genes annotated in D. melanogaster. We also identified a phase 1 intron at a conserved position present in five of the eight glue genes of D. melanogaster, suggesting a common origin for those glue genes. A slightly significant rate of gene turnover was inferred. Both the number of repeats and the repeat sequence were found to diverge rapidly, even between closely related species. We also detected high repeat number variation at the intrapopulation level in D. melanogaster. Conclusion Most conspicuous signs of accelerated evolution are found in the repeat regions of several glue genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1364-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Luc Da Lage
- UMR 9191 Évolution, Génomes, Comportement, Écologie. CNRS, IRD, Université Paris-Sud. Université Paris-Saclay, F-91198, Gif-sur-Yvette, France.
| | - Gregg W C Thomas
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Magalie Bonneau
- UMR 9191 Évolution, Génomes, Comportement, Écologie. CNRS, IRD, Université Paris-Sud. Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
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71
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Wang XR, Wang C, Wang XW, Qian LX, Chi Y, Liu SS, Liu YQ, Wang XW. The functions of caspase in whitefly Bemisia tabaci apoptosis in response to ultraviolet irradiation. INSECT MOLECULAR BIOLOGY 2018; 27:739-751. [PMID: 29892978 DOI: 10.1111/imb.12515] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Whiteflies (Bemisia tabaci) are phloem feeders, and some invasive species are composed of cryptic species complexes that cause extensive crop damage, particularly via the direct transmission of plant viruses. Apoptosis is a type of programmed cell death essential for organismal development and tissue homeostasis. The caspases belong to a family of cysteine proteases that play a central role in the initiation of apoptosis in many organisms. Here, we employed a comprehensive genomics approach to identity caspases in B. tabaci Middle East Asia Minor 1 (MEAM1), an invasive whitefly that carries a cryptic species complex that is devastating to crops. Four caspase genes were identified, and their motif compositions were predicted. Structures were relatively conserved in both putative effector and initiator caspases. Expression patterns of caspase genes differed across insect developmental stages. Three caspase genes were induced immediately after ultraviolet (UV) treatment. Expression levels of Bt-caspase-1 and Bt-caspase-3b increased in the midgut and salivary glands during apoptosis induced by UV treatments, whereas silencing of both genes reduced UV-triggered apoptosis. Our study demonstrates that Bt-caspase-1 and Bt-caspase-3b, respectively, act as putative initiator and effector apoptotic caspases in the MEAM1 whitefly.
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Affiliation(s)
- X-R Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - C Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - X-W Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - L-X Qian
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Y Chi
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - S-S Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Y-Q Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - X-W Wang
- 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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Finet C, Decaras A, Armisén D, Khila A. The achaete-scute complex contains a single gene that controls bristle development in the semi-aquatic bugs. Proc Biol Sci 2018; 285:rspb.2018.2387. [PMID: 30487316 PMCID: PMC6283939 DOI: 10.1098/rspb.2018.2387] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/06/2018] [Indexed: 11/24/2022] Open
Abstract
The semi-aquatic bugs (Heteroptera, Gerromorpha) conquered water surfaces worldwide and diversified to occupy puddles, ponds, streams, lakes, mangroves and even oceans. Critical to this lifestyle is the evolution of sets of hairs that allow these insects to maintain their body weight on the water surface and protect the animals against wetting and drowning. In addition, the legs of these insects are equipped with various grooming combs that are important for cleaning and tidying the hair layers for optimal functional efficiency. Here we show that the hairs covering the legs of water striders represent innervated bristles. Genomic and transcriptomic analyses revealed that in water striders the achaete–scute complex, known to control bristle development in flies, contains only the achaete–scute homologue (ASH) gene owing to the loss of the gene asense. Using RNA interference, we show that ASH plays a pivotal role in the development of both bristles and grooming combs in water striders. Our data suggest that the ASH locus may have contributed to the adaptation to water surface lifestyle through shaping the hydrophobic bristles that prevent water striders from wetting and allow them to exploit water surface tension.
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Affiliation(s)
- Cédric Finet
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69364 Lyon, France
| | - Amélie Decaras
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69364 Lyon, France
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69364 Lyon, France
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie, 69364 Lyon, France
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Fu X, Li J, Tian Y, Quan W, Zhang S, Liu Q, Liang F, Zhu X, Zhang L, Wang D, Hu J. Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. Gigascience 2018; 6:1-7. [PMID: 29186486 PMCID: PMC5751067 DOI: 10.1093/gigascience/gix112] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/15/2017] [Indexed: 01/27/2023] Open
Abstract
Background Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.
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Affiliation(s)
- Xinhua Fu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430000, China
| | - Jingjing Li
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Yu Tian
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Weipeng Quan
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Shu Zhang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Qian Liu
- Institute for Genomic Medicine, Columbia University, 116th Street and Broadway, New York, NY 10032, USA
| | - Fan Liang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Shizishan Street, Hongshan District, Wuhan, Hubei 430000, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Shangxiadian Road, Cangshan District, Fuzhou 350002, China
| | - Depeng Wang
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Jiang Hu
- Nextomics Biosciences Institute, Biolake, No. 666 Gaoxin Road, Wuhan, Hubei 430000, China
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Llonga N, Ylla G, Bau J, Belles X, Piulachs MD. Diversity of piRNA expression patterns during the ontogeny of the German cockroach. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:288-295. [DOI: 10.1002/jez.b.22815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/15/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Natalia Llonga
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
| | - Guillem Ylla
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
- Department of Microbiology and Cell Science; Institute for Food and Agricultural Sciences, Genetics Institute; University of Florida; Gainesville Florida
| | - Josep Bau
- Department of Biosciences; University of Vic - Central University of Catalonia; Vic, Barcelona Spain
| | - Xavier Belles
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
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Yin C, Li M, Hu J, Lang K, Chen Q, Liu J, Guo D, He K, Dong Y, Luo J, Song Z, Walters JR, Zhang W, Li F, Chen X. The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum. BMC Genomics 2018; 19:420. [PMID: 29848290 PMCID: PMC5977540 DOI: 10.1186/s12864-018-4783-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/11/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host's immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host's immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown. RESULTS We report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion. CONCLUSIONS The microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide new insights into the polyembryony and immune evasion.
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Affiliation(s)
- Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Jian Hu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Kun Lang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Qiming Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Jinding Liu
- College of Information Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dianhao Guo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Yipei Dong
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Zhenkun Song
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - James R. Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66046 USA
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275 China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Xuexin Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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Chen YH, Schoville SD. Editorial overview: Ecology: Ecological adaptation in agroecosystems: novel opportunities to integrate evolutionary biology and agricultural entomology. CURRENT OPINION IN INSECT SCIENCE 2018; 26:iv-viii. [PMID: 29764669 DOI: 10.1016/j.cois.2018.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI, USA
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77
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Pratheepa M, Venkatesan T, Gracy G, Jalali SK, Rangheswaran R, Antony JC, Rai A. An Integrated Molecular Database on Indian Insects. Bioinformation 2018; 14:42-47. [PMID: 29618898 PMCID: PMC5879950 DOI: 10.6026/97320630014042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 11/23/2022] Open
Abstract
MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. AVAILABILITY http://cib.res.in/.
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Affiliation(s)
- Maria Pratheepa
- ICAR-National Bureau of Agricultural Insect Resources, H.A. Farm Post, P.Bag No: 2491, Bellary Road, Hebbal, Bengaluru - 560 024. India
| | - Thiruvengadam Venkatesan
- ICAR-National Bureau of Agricultural Insect Resources, H.A. Farm Post, P.Bag No: 2491, Bellary Road, Hebbal, Bengaluru - 560 024. India
| | - Gandhi Gracy
- ICAR-National Bureau of Agricultural Insect Resources, H.A. Farm Post, P.Bag No: 2491, Bellary Road, Hebbal, Bengaluru - 560 024. India
| | - Sushil Kumar Jalali
- ICAR-National Bureau of Agricultural Insect Resources, H.A. Farm Post, P.Bag No: 2491, Bellary Road, Hebbal, Bengaluru - 560 024. India
| | - Rajagopal Rangheswaran
- ICAR-National Bureau of Agricultural Insect Resources, H.A. Farm Post, P.Bag No: 2491, Bellary Road, Hebbal, Bengaluru - 560 024. India
| | - Jomin Cruz Antony
- Department of Computer Science, Jain University, Bengaluru - 560 027, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistical, Research Institute, New Delhi - 110 012, India
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78
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Triant DA, Cinel SD, Kawahara AY. Lepidoptera genomes: current knowledge, gaps and future directions. CURRENT OPINION IN INSECT SCIENCE 2018; 25:99-105. [PMID: 29602369 DOI: 10.1016/j.cois.2017.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 06/08/2023]
Abstract
Butterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders. With recent advances in genomics, new Lepidoptera genomes are regularly being sequenced, and many of them are playing principal roles in genomics studies, particularly in the fields of phylo-genomics and functional genomics. Thus far, assembled genomes are only available for <10 of the 43 Lepidoptera superfamilies. Nearly all are model species, found in the speciose clade Ditrysia. Community support for Lepidoptera genomics is growing with successful management and dissemination of data and analytical tools in centralized databases. With genomic studies quickly becoming integrated with ecological and evolutionary research, the Lepidoptera community will unquestionably benefit from new high-quality reference genomes that are more evenly distributed throughout the order.
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Affiliation(s)
- Deborah A Triant
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| | - Scott D Cinel
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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79
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Wiegmann BM, Richards S. Genomes of Diptera. CURRENT OPINION IN INSECT SCIENCE 2018; 25:116-124. [PMID: 29602357 DOI: 10.1016/j.cois.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.
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Affiliation(s)
- Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77006, United States
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80
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Qiu L, Wang P, Wu T, Li B, Wang X, Lei C, Lin Y, Zhao J, Ma W. Downregulation of Chilo suppressalis alkaline phosphatase genes associated with resistance to three transgenic Bacillus thuringiensis rice lines. INSECT MOLECULAR BIOLOGY 2018; 27:83-89. [PMID: 28940938 DOI: 10.1111/imb.12349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Insecticidal crystal (Cry) proteins produced by the bacterium Bacillus thuringiensis are highly toxic to lepidopteran pests. Strains of transgenic rice expressing cry genes have been developed that are resistant to rice pests. Understanding the mode of action of Cry toxins in rice pests will improve our ability to use them effectively as insecticides. In this study, we tested the hypothesis that alkaline phosphatases (ALPs) are involved in Cry1A, Cry2Aa and Cry1Ca toxicity in Chilo suppressalis, an important insect pest of rice crops in China. We first cloned three novel C. suppressalis alps (Csalps) from the larval midgut of C. suppressalis. RNA interference knockdown of six different Csalp genes (Csalp1, Csalp2, Csalp3, Csalp4, Csalp5 and Csalp6) showed that knockdown of three of these, Csalp1, Csalp2 and Csalp4, reduced larval mortality to the transgenic rice strain TT51, which expresses a fusion protein of Cry1Ab and Cry1Ac, whereas suppression of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp6 transcripts decreased the susceptibility of larvae to the transgenic rice strain T2A-1, which expresses cry2Aa. Moreover, downregulation of Csalp1, Csalp2, Csalp3, Csalp4 and Csalp5 transcripts conferred significant tolerance to the transgenic rice strain T1C-19, which expresses cry1Ca. These results suggest that these ALPs play a key role in the toxicity of Cry1A, Cry2A and Cry1C to C. suppressalis.
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Affiliation(s)
- L Qiu
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - P Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - T Wu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - B Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - X Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - C Lei
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Y Lin
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
| | - J Zhao
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - W Ma
- National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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81
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Chen L, Lang K, Bi S, Luo J, Liu F, Ye X, Xu J, He K, Li F, Ye G, Chen X. WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-9. [PMID: 30219838 PMCID: PMC6146128 DOI: 10.1093/database/bay081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/10/2018] [Indexed: 01/30/2023]
Abstract
Insect pests reduce yield and cause economic losses, which are major problems in agriculture. Parasitic wasps are the natural enemies of many agricultural pests and thus have been widely used as biological control agents. Plants, phytophagous insects and parasitic wasps form a tritrophic food chain. Understanding the interactions in this tritrophic system should be helpful for developing parasitic wasps for pest control and deciphering the mechanisms of parasitism. However, the genomic resources for this tritrophic system are not well organized. Here, we describe the WaspBase, a new database that contains 573 transcriptomes of 35 parasitic wasps and the genomes of 12 parasitic wasps, 5 insect hosts and 8 plants. In addition, we identified long non-coding RNA, untranslated regions and 25 widely studied gene families from the genome and transcriptome data of these species. WaspBase provides conventional web services such as Basic Local Alignment Search Tool, search and download, together with several widely used tools such as profile hidden Markov model, Multiple Alignment using Fast Fourier Transform, automated alignment trimming and JBrowse. We also present a collection of active researchers in the field of parasitic wasps, which should be useful for constructing scientific networks in this field.
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Affiliation(s)
- Longfei Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Kun Lang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China.,Anhui Agricultural University, 130 Changjiangxilu, Hefei, Anhui, China
| | - Shoudong Bi
- Anhui Agricultural University, 130 Changjiangxilu, Hefei, Anhui, China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Xinhai Ye
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Jiadan Xu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Gongyin Ye
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
| | - Xuexin Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, China
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Chen J, Zhang J, Lin M, Dong W, Guo X, Dong Y, Wang Z, Zhang L, Chen F. MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). Database (Oxford) 2018; 2018:5136497. [PMID: 30339215 PMCID: PMC6195103 DOI: 10.1093/database/bay113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/05/2018] [Accepted: 09/24/2018] [Indexed: 01/18/2023]
Abstract
Maca (Lepidium meyenii), a Brassicaceae herb plant originated from Andean mountains, has attracted wide interests due to its unique health benefits in reproduction and fertility. Because of its adaptation to the 4000 m high-altitude harsh environment, maca is attracting more and more attention from both crop breeders and basic biologists. After our previous release of the maca genome sequence, there's a growing need to store, query, analyze and integrate various maca resources efficiently. Here, we created Maca Genome Hub (MGH), a genomics and genetics database of maca. Currently, the MGH V1.0 harbors the genome sequence, predicted coding sequences and protein sequences, various annotations, markers and expression data. For the maca research community, we also provided the publications, researchers and related news. MGH is designed to enable users' easy access to analyze, retrieve and visualize the genomic or genetic information through a series of online tools, including the Basic Local Alignment Search Tool, the JBrowse, the query system, the synteny tool and the data downloads. These integrated heterogeneous data, tools and interfaces in MGH allow efficient mining of the latest genomics and genetics data. We hope that MGH will accelerate the research and development in maca.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiawei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meigui Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyue Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Dong
- Biological Big Data College, Yunnan Agricultural University, Kunming, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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83
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Poelchau MF, Chen MJM, Lin YY, Childers CP. Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes. Methods Mol Biol 2018; 1757:557-577. [PMID: 29761470 DOI: 10.1007/978-1-4939-7737-6_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The i5k Workspace@NAL is a genome database tailored toward newly sequenced arthropod genomes and their research communities. With 56 arthropod genomes and counting, the i5k Workspace strives to facilitate public data access, visualization, and community curation across arthropod species. Any researcher with an arthropod genome project who would like to take advantage of the i5k Workspace facilities is encouraged to submit their data. In this chapter, we explain how to use the i5k Workspace@NAL to submit, find, and improve arthropod genomics data.
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Affiliation(s)
- Monica F Poelchau
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD, USA.
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Christopher P Childers
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD, USA.
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84
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Almeida Garcia R, Lima Pepino Macedo L, Cabral do Nascimento D, Gillet FX, Moreira-Pinto CE, Faheem M, Moreschi Basso AM, Mattar Silva MC, Grossi-de-Sa MF. Nucleases as a barrier to gene silencing in the cotton boll weevil, Anthonomus grandis. PLoS One 2017; 12:e0189600. [PMID: 29261729 PMCID: PMC5738047 DOI: 10.1371/journal.pone.0189600] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) approaches have been applied as a biotechnological tool for controlling plant insect pests via selective gene down regulation. However, the inefficiency of RNAi mechanism in insects is associated with several barriers, including dsRNA delivery and uptake by the cell, dsRNA interaction with the cellular membrane receptor and dsRNA exposure to insect gut nucleases during feeding. The cotton boll weevil (Anthonomus grandis) is a coleopteran in which RNAi-mediated gene silencing does not function efficiently through dsRNA feeding, and the factors involved in the mechanism remain unknown. Herein, we identified three nucleases in the cotton boll weevil transcriptome denoted AgraNuc1, AgraNuc2, and AgraNuc3, and the influences of these nucleases on the gene silencing of A. grandis chitin synthase II (AgraChSII) were evaluated through oral dsRNA feeding trials. A phylogenetic analysis showed that all three nucleases share high similarity with the DNA/RNA non-specific endonuclease family of other insects. These nucleases were found to be mainly expressed in the posterior midgut region of the insect. Two days after nuclease RNAi-mediated gene silencing, dsRNA degradation by the gut juice was substantially reduced. Notably, after nucleases gene silencing, the orally delivered dsRNA against the AgraChSII gene resulted in improved gene silencing efficiency when compared to the control (non-silenced nucleases). The data presented here demonstrates that A. grandis midgut nucleases are effectively one of the main barriers to dsRNA delivery and emphasize the need to develop novel RNAi delivery strategies focusing on protecting the dsRNA from gut nucleases and enhancing its oral delivery and uptake to crop insect pests.
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Affiliation(s)
- Rayssa Almeida Garcia
- Brasilia Federal University (UnB), Brasília - CEP, Brasília, Federal District, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District, Brazil
| | | | | | | | - Clidia Eduarda Moreira-Pinto
- Brasilia Federal University (UnB), Brasília - CEP, Brasília, Federal District, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District, Brazil
| | - Muhammad Faheem
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District, Brazil
| | | | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, Federal District, Brazil
- Catholic University of Brasília, CEP, Brasília, Federal District, Brazil
- * E-mail:
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85
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He K, Sun Y, Xiao H, Ge C, Li F, Han Z. Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis. RNA (NEW YORK, N.Y.) 2017; 23:1817-1833. [PMID: 28860304 PMCID: PMC5689003 DOI: 10.1261/rna.061408.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/18/2017] [Indexed: 05/30/2023]
Abstract
The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of suppressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dual-luciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titer of 20-hydroxyecdysone (20E), induced mortality, and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity.
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Affiliation(s)
- Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yang Sun
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Plant Protection, Jiangxi Academy of Agricultural Science, Nanchang 330200, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun 336000, China
| | - Chang Ge
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhaojun Han
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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86
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Liu F, Guo D, Yuan Z, Chen C, Xiao H. Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella. Sci Rep 2017; 7:15870. [PMID: 29158595 PMCID: PMC5696462 DOI: 10.1038/s41598-017-16057-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/06/2017] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNA (lncRNA) is a class of noncoding RNA >200 bp in length that has essential roles in regulating a variety of biological processes. Here, we constructed a computational pipeline to identify lncRNA genes in the diamondback moth (Plutella xylostella), a major insect pest of cruciferous vegetables. In total, 3,324 lncRNAs corresponding to 2,475 loci were identified from 13 RNA-Seq datasets, including samples from parasitized, insecticide-resistant strains and different developmental stages. The identified P. xylostella lncRNAs had shorter transcripts and fewer exons than protein-coding genes. Seven out of nine randomly selected lncRNAs were validated by strand-specific RT-PCR. In total, 54-172 lncRNAs were specifically expressed in the insecticide resistant strains, among which one lncRNA was located adjacent to the sodium channel gene. In addition, 63-135 lncRNAs were specifically expressed in different developmental stages, among which three lncRNAs overlapped or were located adjacent to the metamorphosis-associated genes. These lncRNAs were either strongly or weakly co-expressed with their overlapping or neighboring mRNA genes. In summary, we identified thousands of lncRNAs and presented evidence that lncRNAs might have key roles in conferring insecticide resistance and regulating the metamorphosis development in P. xylostella.
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Affiliation(s)
- Feiling Liu
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Dianhao Guo
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhuting Yuan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China.
- The Center for Translational Medicine, Yichun University, Yichun, 336000, China.
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87
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Mongelli V, Saleh MC. Bugs Are Not to Be Silenced: Small RNA Pathways and Antiviral Responses in Insects. Annu Rev Virol 2017; 3:573-589. [PMID: 27741406 DOI: 10.1146/annurev-virology-110615-042447] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Like every other organism on Earth, insects are infected with viruses, and they rely on RNA interference (RNAi) mechanisms to circumvent viral infections. A remarkable characteristic of RNAi is that it is both broadly acting, because it is triggered by double-stranded RNA molecules derived from virtually any virus, and extremely specific, because it targets only the particular viral sequence that initiated the process. Reviews covering the different facets of the RNAi antiviral immune response in insects have been published elsewhere. In this review, we build a framework to guide future investigation. We focus on the remaining questions and avenues of research that need to be addressed to move the field forward, including issues such as the activity of viral suppressors of RNAi, comparative genomics, the development of detailed maps of the subcellular localization of viral replication complexes with the RNAi machinery, and the regulation of the antiviral RNAi response.
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Affiliation(s)
- Vanesa Mongelli
- Viruses and RNA Interference Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France;
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France;
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88
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Ding S, Wang S, He K, Jiang M, Li F. Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects. BMC Genomics 2017; 18:848. [PMID: 29110701 PMCID: PMC5674736 DOI: 10.1186/s12864-017-4234-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown. RESULTS We identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2-93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22-73 bp) were longer than perfect SSRs (16-30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level. CONCLUSION Millions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.
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Affiliation(s)
- Simin Ding
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Entry-exit Inspection and Quarantine Bureau, Shanghai, 200135 China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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89
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Alonso J, Martinez M. Insights into the molecular evolution of peptidase inhibitors in arthropods. PLoS One 2017; 12:e0187643. [PMID: 29108008 PMCID: PMC5673224 DOI: 10.1371/journal.pone.0187643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
Peptidase inhibitors are key proteins involved in the control of peptidases. In arthropods, peptidase inhibitors modulate the activity of peptidases involved in endogenous physiological processes and peptidases of the organisms with which they interact. Exploring available arthropod genomic sequences is a powerful way to obtain the repertoire of peptidase inhibitors in every arthropod species and to understand the evolutionary mechanisms involved in the diversification of this kind of proteins. A genomic comparative analysis of peptidase inhibitors in species belonging to different arthropod taxonomic groups was performed. The results point out: i) species or clade-specific presence is shown for several families of peptidase inhibitors; ii) multidomain peptidase inhibitors are commonly found in many peptidase inhibitor families; iii) several families have a wide range of members in different arthropod species; iv) several peptidase inhibitor families show species-specific (or clade-specific) gene family expansions; v) functional divergence may be assumed for particular clades; vi) passive expansions may be used by natural selection to fix adaptations. In conclusion, conservation and divergence of duplicated genes and the potential recruitment as peptidase inhibitors of proteins from other families are the main mechanisms used by arthropods to fix diversity. This diversity would be associated to the control of target peptidases and, as consequence, to adapt to specific environments.
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Affiliation(s)
- Joaquin Alonso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
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90
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Zhao J, Zhou Y, Li X, Cai W, Hua H. Silencing of juvenile hormone epoxide hydrolase gene (Nljheh) enhances short wing formation in a macropterous strain of the brown planthopper, Nilaparvata lugens. JOURNAL OF INSECT PHYSIOLOGY 2017; 102:18-26. [PMID: 28867330 DOI: 10.1016/j.jinsphys.2017.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
The rice brown planthopper, Nilaparvata lugens, is an important migratory pest in many rice planting areas of Asia. The typical wing dimorphism of N. lugens gives them flexibility to adapt to different environmental cues. As an important hormone in the insect's endocrine regulation, juvenile hormone (JH) has previously been shown to participate in the wing morph determination of N. lugens. In this paper, we investigated the possible wing morph determination roles of two JH metabolic enzymes, JH esterase (JHE) and JH epoxide hydrolase (JHEH). A 1957-bp full-length cDNA sequence encoding JHEH in N. lugens (NlJHEH) was first cloned from a hemipteran insect. Except for an uncertain transmembrane segment prediction, the deduced 454-amino-acid sequence of Nljheh has all of the conserved domains of JHEHs such as the H147GWP150, Tyr293 and Tyr368 motif corresponding to the oxyanion hole and the residues Asp222, Glu398, and His425 in the catalytic triad. qRT-PCR results showed that both Nljhe and Nljheh had different expression timeframes between a predominantly brachypterous strain (BS) and a macropterous strain (MS) of N. lugens, indicating that these two enzymes may participate in wing dimorphism regulation in brown planthopper. Silencing Nljheh expression by dsRNA injection enhanced short wing formation in the macropterous strain of N. lugens, while the brachypterizing individuals were mainly females. Compared to the dsgfp injection control, silencing Nljhe had no brachypterizing effect. Our results indicated that NlJHEH plays an important role in the wing morph determination of N. lugens.
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Affiliation(s)
- Jing Zhao
- Hubei Insect Resources Utilisation and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yunlong Zhou
- Hubei Insect Resources Utilisation and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiang Li
- Hubei Insect Resources Utilisation and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wanlun Cai
- Hubei Insect Resources Utilisation and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hongxia Hua
- Hubei Insect Resources Utilisation and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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91
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Perspectives on Gene Regulatory Network Evolution. Trends Genet 2017; 33:436-447. [PMID: 28528721 DOI: 10.1016/j.tig.2017.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 11/23/2022]
Abstract
Animal development proceeds through the activity of genes and their cis-regulatory modules (CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here various aspects of GRN evolution and argue that developmental system drift (DSD), in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution. Advances in methods to discover related CRMs in diverse insect species, a critical requirement for detailed GRN characterization, are also described.
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92
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Sun Y, Huang S, Wang S, Guo D, Ge C, Xiao H, Jie W, Yang Q, Teng X, Li F. Large-scale identification of differentially expressed genes during pupa development reveals solute carrier gene is essential for pupal pigmentation in Chilo suppressalis. JOURNAL OF INSECT PHYSIOLOGY 2017; 98:117-125. [PMID: 28041944 DOI: 10.1016/j.jinsphys.2016.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/22/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
Insects undergo metamorphosis, involving an abrupt change in body structure through cell growth and differentiation. Rice stem stripped borer (SSB), Chilo suppressalis, is one of the most destructive rice pests. However, little is known about the regulation mechanism of metamorphosis development in this notorious insect pest. Here, we studied the expression of 22,197 SSB genes at seven time points during pupa development with a customized microarray, identifying 622 differentially expressed genes (DEG) during pupa development. Gene ontology (GO) analysis of these DEGs indicated that the genes related to substance metabolism were highly expressed in the early pupa, which participate in the physiological processes of larval tissue disintegration at these stages. In comparison, highly expressed genes in the late pupal stages were mainly associated with substance biosynthesis, consistent with adult organ formation at these stages. There were 27 solute carrier (SLC) genes that were highly expressed during pupa development. We knocked down SLC22A3 at the prepupal stage, demonstrating that silencing SLC22A3 induced a deficiency in pupa stiffness and pigmentation. The RNAi-treated individuals had white and soft pupa, suggesting that this gene has an essential role in pupal development.
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Affiliation(s)
- Yang Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuijin Huang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Science, Nanchang 330200, China
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Entry-exit Inspection and Quarantine Bureau, Shanghai 200135, China
| | - Dianhao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chang Ge
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huamei Xiao
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wencai Jie
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiupu Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaolu Teng
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Li
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
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93
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Deep sequencing of the prothoracic gland transcriptome reveals new players in insect ecdysteroidogenesis. PLoS One 2017; 12:e0172951. [PMID: 28257485 PMCID: PMC5336252 DOI: 10.1371/journal.pone.0172951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/13/2017] [Indexed: 12/28/2022] Open
Abstract
Ecdysteroids are steroid hormones that induce molting and determine developmental timing in arthropods. In insect larva, the prothoracic gland (PG) is a major organ for ecdysone synthesis and release. Released ecdysone is converted into the active form, 20-hydroxyecdysone (20E) in the peripheral tissues. All processes from ecdysone synthesis and release from the PG to its conversion to 20E are called ecdysteroidogenesis and are under the regulation of numerous factors expressed in the PG and peripheral tissues. Classical genetic approaches and recent transcriptomic screening in the PG identified several genes responsible for ecdysone synthesis and release, whereas the regulatory mechanism remains largely unknown. We analyzed RNA-seq data of the silkworm Bombyx mori PG and employed the fruit fly Drosophila melanogaster GAL4/UAS binary RNAi system to comprehensively screen for genes involved in ecdysone synthesis and/or release. We found that the genes encoding δ-aminolevulinic acid synthase (CG3017/alas) and putative NAD kinase (CG33156) were highly expressed in the PG of both B. mori and D. melanogaster. Neither alas nor CG33156 RNAi-induced larvae could enter into the pupal stage, and they had a lower abundance of the active form ecdysteroids in their prolonged larval stage. These results demonstrated that alas and CG33156 are indispensable for ecdysteroidogenesis.
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94
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Lin X, Zhang L, Jiang Y. Distinct Roles of Met and Interacting Proteins on the Expressions of takeout Family Genes in Brown Planthopper. Front Physiol 2017; 8:100. [PMID: 28270774 PMCID: PMC5318429 DOI: 10.3389/fphys.2017.00100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/07/2017] [Indexed: 11/17/2022] Open
Abstract
The takeout family genes encode relatively small proteins that are related to olfaction and are regulated by juvenile hormone (JH). The takeout genes modulate various physiological processes, such as behavioral plasticity in the migratory locust Locusta migraloria and feeding and courtship behaviors in Drosophila. Therefore, to understand the regulatory mechanism of these physiological processes, it is important to study the expressions of the takeout genes that are regulated by JH signaling. We used quantitative real-time PCR (qRTPCR) to study the role of JH signaling in the regulation of the takeout family genes in the brown planthopper Nilaparvata lugens (N. lugens) through the application of Juvenile hormone III (JHIII) and the down-regulation of key genes in the JH signaling pathway. The topical application of JHIII induced the expressions of most of the takeout family genes, and their expressions decreased 2 and 3 days after the JHIII application. Down-regulating the brown planthopper JH receptor NlMethoprene-tolerant (NlMet) and its interacting partners, NlTaiman (NlTai) and Nlß-Ftz-F1 (Nlß-Ftz), through RNAi, exhibited distinct effects on the expressions of the takeout family genes. The down-regulation of NlMet and NlKrüppel-homolog 1 (NlKr-h1) increased the expressions of the takeout family genes, while the down-regulation of the Met interacting partners NlTai and Nlß-Ftz decreased the expressions of most of the takeout family genes. This work advanced our understanding of the molecular function and the regulatory mechanism of JH signaling.
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Affiliation(s)
- Xinda Lin
- Department of Biology, College of Life Sciences, China Jiliang University Hangzhou, China
| | - Ling Zhang
- Department of Biology, College of Life Sciences, China Jiliang University Hangzhou, China
| | - Yanyun Jiang
- Department of Biology, College of Life Sciences, China Jiliang University Hangzhou, China
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95
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He K, Lin K, Wang G, Li F. Genome Sizes of Nine Insect Species Determined by Flow Cytometry and k-mer Analysis. Front Physiol 2016; 7:569. [PMID: 27932995 PMCID: PMC5121235 DOI: 10.3389/fphys.2016.00569] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 11/08/2016] [Indexed: 11/13/2022] Open
Abstract
The flow cytometry method was used to estimate the genome sizes of nine agriculturally important insects, including two coleopterans, five Hemipterans, and two hymenopterans. Among which, the coleopteran Lissorhoptrus oryzophilus (Kuschel) had the largest genome of 981 Mb. The average genome size was 504 Mb, suggesting that insects have a moderate-size genome. Compared with the insects in other orders, hymenopterans had small genomes, which were averagely about ~200 Mb. We found that the genome sizes of four insect species were different between male and female, showing the organismal complexity of insects. The largest difference occurred in the coconut leaf beetle Brontispa longissima (Gestro). The male coconut leaf beetle had a 111 Mb larger genome than females, which might be due to the chromosome number difference between the sexes. The results indicated that insect invasiveness was not related to genome size. We also determined the genome sizes of the small brown planthopper Laodelphax striatellus (Fallén) and the parasitic wasp Macrocentrus cingulum (Brischke) using k-mer analysis with Illunima Solexa sequencing data. There were slight differences in the results from the two methods. k-mer analysis indicated that the genome size of L. striatellus was 500–700 Mb and that of M. cingulum was ~150 Mb. In all, the genome sizes information presented here should be helpful for designing the genome sequencing strategy when necessary.
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Affiliation(s)
- Kang He
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University Nanjing, China
| | - Kejian Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing, China
| | - Fei Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural UniversityNanjing, China; Ministry of Agriculture, Key Lab of Agricultural Entomology and Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
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96
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Urbansky S, González Avalos P, Wosch M, Lemke S. Folded gastrulation and T48 drive the evolution of coordinated mesoderm internalization in flies. eLife 2016; 5. [PMID: 27685537 PMCID: PMC5042651 DOI: 10.7554/elife.18318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022] Open
Abstract
Gastrulation constitutes a fundamental yet diverse morphogenetic process of metazoan development. Modes of gastrulation range from stochastic translocation of individual cells to coordinated infolding of an epithelial sheet. How such morphogenetic differences are genetically encoded and whether they have provided specific developmental advantages is unclear. Here we identify two genes, folded gastrulation and t48, which in the evolution of fly gastrulation acted as a likely switch from an ingression of individual cells to the invagination of the blastoderm epithelium. Both genes are expressed and required for mesoderm invagination in the fruit fly Drosophila melanogaster but do not appear during mesoderm ingression of the midge Chironomus riparius. We demonstrate that early expression of either or both of these genes in C.riparius is sufficient to invoke mesoderm invagination similar to D.melanogaster. The possible genetic simplicity and a measurable increase in developmental robustness might explain repeated evolution of similar transitions in animal gastrulation. DOI:http://dx.doi.org/10.7554/eLife.18318.001 In animals, gastrulation is a period of time in early development during which a sphere of cells is reorganized into an embryo with cells arranged into three distinct layers (called germ layers). The process has changed substantially during the course of evolution and thus provides a great experimental system to investigate the genetic basis for differences in animal form and shape. As an example, true flies use at least two different mechanisms to make the middle germ layer (the mesoderm). In both cases, the mesoderm is made up of cells that move inwards from the boundary of the outer germ layer. In midges and some other flies, these cells migrate individually, while in others including fruit flies, the cells move together as a sheet. Fruit flies and midges shared their last common ancestor 250 million years ago and although the genes that make the mesoderm in fruit flies are well understood, little is known about how the mesoderm forms in midges. Urbansky, González Avalos et al. investigated which genes were responsible for the evolutionary transition between the different types of cell migration seen in flies. The experiments identified two genes – called folded gastrulation and t48 – that seem to operate as a simple switch between the two ways that mesoderm cells migrate. Both of these genes are active in fruit fly embryos and are required for the group migration of mesoderm cells. However, the genes do not appear to play a major role in the movement of individual mesoderm cells in midges. Further experiments demonstrate that switching on these genes in midge embryos is sufficient to invoke group mesoderm cell migrations similar to those seen in fruit flies. These findings show that it is possible to identify genetic changes that underlie substantial differences in animal form and shape over hundred million of years. The ease by which Urbansky, González Avalos et al. were able to switch between the two types of mesoderm migration might explain why similar transitions in gastrulation have evolved repeatedly in animals. The next step is to test this hypothesis in other animals. DOI:http://dx.doi.org/10.7554/eLife.18318.002
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Affiliation(s)
- Silvia Urbansky
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Paula González Avalos
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
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97
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Perilla-Henao LM, Casteel CL. Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1163. [PMID: 27555855 PMCID: PMC4977473 DOI: 10.3389/fpls.2016.01163] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/20/2016] [Indexed: 05/22/2023]
Abstract
Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant-virus-vector interactions has flourished in recent years, plant-bacteria-vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant-bacteria-vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and 'Candidatus Phytoplasma spp.'. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector-plant-bacteria interactions.
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Affiliation(s)
| | - Clare L. Casteel
- Department of Plant Pathology, University of California at Davis, Davis, CAUSA
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98
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Su C, Tu G, Huang S, Yang Q, Shahzad MF, Li F. Genome-wide analysis of chitinase genes and their varied functions in larval moult, pupation and eclosion in the rice striped stem borer, Chilo suppressalis. INSECT MOLECULAR BIOLOGY 2016; 25:401-412. [PMID: 27080989 DOI: 10.1111/imb.12227] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Some insect chitinases are required to degrade chitin and ensure successful metamorphosis. Although chitinase genes have been well characterized in several model insects, no reports exist for the rice striped stem borer, Chilo suppressalis, a highly destructive pest that causes huge yield losses in rice production. Here, we conducted a genome-level analysis of chitinase genes in C. suppressalis. After amplification of full-length transcripts with rapid amplification of cDNA ends, we identified 12 chitinase genes in C. suppressalis. All these genes had the conserved domains and motifs of glycoside hydrolase family 18 and grouped phylogenetically into five subgroups. C. suppressalis chitinase 1 (CsCht1) was highly expressed in late pupae, whereas CsCht3 was abundant in early pupae. Both CsCht2 and CsCht4 were highly expressed in larvae. CsCht2 was abundant specifically in the third-instar larvae and CsCht4 showed periodic high expression in 2- to 5-day-old larvae in each instar. Tissue specific expression analysis indicated that CsCht1 and CsCht3 were highly expressed in epidermis whereas CsCht2 and CsCht4 were specifically abundant in the midgut. Knockdown of CsCht1 resulted in adults with curled wings, indicating that CsCht1 might have an important role in wing expansion. Silencing of CsCht2 or CsCht4 arrested moulting, suggesting essential roles in larval development. When the expression of CsCht3 was interfered, defects in pupation occurred. Overall, we provide here the first catalogue of chitinase genes in the rice striped stem borer and have elucidated the functions of four chitinases in metamorphosis.
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Affiliation(s)
- C Su
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - G Tu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - S Huang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Science, Nanchang, China
| | - Q Yang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - M F Shahzad
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - F Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- MOA Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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99
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Rigden DJ, Fernández-Suárez XM, Galperin MY. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic Acids Res 2016; 44:D1-6. [PMID: 26740669 PMCID: PMC4702933 DOI: 10.1093/nar/gkv1356] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 01/21/2023] Open
Abstract
The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | | | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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100
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van Kleeff PJM, Galland M, Schuurink RC, Bleeker PM. Small RNAs from Bemisia tabaci Are Transferred to Solanum lycopersicum Phloem during Feeding. FRONTIERS IN PLANT SCIENCE 2016; 7:1759. [PMID: 27933079 PMCID: PMC5121246 DOI: 10.3389/fpls.2016.01759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/08/2016] [Indexed: 05/09/2023]
Abstract
The phloem-feeding whitefly Bemisia tabaci is a serious pest to a broad range of host plants, including many economically important crops such as tomato. These insects serve as a vector for various devastating plant viruses. It is known that whiteflies are capable of manipulating host-defense responses, potentially mediated by effector molecules in the whitefly saliva. We hypothesized that, beside putative effector proteins, small RNAs (sRNA) are delivered by B. tabaci into the phloem, where they may play a role in manipulating host plant defenses. There is already evidence to suggest that sRNAs can mediate the host-pathogen dialogue. It has been shown that Botrytis cinerea, the causal agent of gray mold disease, takes advantage of the plant sRNA machinery to selectively silence host genes involved in defense signaling. Here we identified sRNAs originating from B. tabaci in the phloem of tomato plants on which they are feeding. sRNAs were isolated and sequenced from tomato phloem of whitefly-infested and control plants as well as from the nymphs themselves, control leaflets, and from the infested leaflets. Using stem-loop RT-PCR, three whitefly sRNAs have been verified to be present in whitefly-infested leaflets that were also present in the whitefly-infested phloem sample. Our results show that whitefly sRNAs are indeed present in tomato tissues upon feeding, and they appear to be mobile in the phloem. Their role in the host-insect interaction can now be investigated.
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