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Fan X, Gao X, Zang H, Liu Z, Jing X, Liu X, Guo S, Jiang H, Wu Y, Huang Z, Chen D, Guo R. Transcriptional dynamics and regulatory function of milRNAs in Ascosphaera apis invading Apis mellifera larvae. Front Microbiol 2024; 15:1355035. [PMID: 38650880 PMCID: PMC11033319 DOI: 10.3389/fmicb.2024.1355035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
In the present study, small RNA (sRNA) data from Ascosphaera apis were filtered from sRNA-seq datasets from the gut tissues of A. apis-infected Apis mellifera ligustica worker larvae, which were combined with the previously gained sRNA-seq data from A. apis spores to screen differentially expressed milRNAs (DEmilRNAs), followed by trend analysis and investigation of the DEmilRNAs in relation to significant trends. Additionally, the interactions between the DEmilRNAs and their target mRNAs were verified using a dual-luciferase reporter assay. In total, 974 A. apis milRNAs were identified. The first base of these milRNAs was biased toward U. The expression of six milRNAs was confirmed by stem-loop RT-PCR, and the sequences of milR-3245-y and milR-10285-y were validated using Sanger sequencing. These miRNAs grouped into four significant trends, with the target mRNAs of DEmilRNAs involving 42 GO terms and 120 KEGG pathways, such as the fungal-type cell wall and biosynthesis of secondary metabolites. Further investigation demonstrated that 299 DEmilRNAs (novel-m0011-3p, milR-10048-y, bantam-y, etc.) potentially targeted nine genes encoding secondary metabolite-associated enzymes, while 258 (milR-25-y, milR-14-y, milR-932-x, etc.) and 419 (milR-4561-y, milR-10125-y, let-7-x, etc.) DEmilRNAs putatively targeted virulence factor-encoded genes and nine genes involved in the MAPK signaling pathway, respectively. Additionally, the interaction between ADM-B and milR-6882-x, as well as between PKIA and milR-7009-x were verified. Together, these results not only offer a basis for clarifying the mechanisms underlying DEmilRNA-regulated pathogenesis of A. apis and a novel insight into the interaction between A. apis and honey bee larvae, but also provide candidate DEmilRNA-gene axis for further investigation.
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Affiliation(s)
- Xiaoxue Fan
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuze Gao
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Zang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhitan Liu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Jing
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyu Liu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sijia Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibin Jiang
- Jilin Apicultural Research Institute, Jilin, China
| | - Ying Wu
- Jilin Apicultural Research Institute, Jilin, China
| | - Zhijian Huang
- Animal Husbandry Terminus of Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu, China
| | - Dafu Chen
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
- National and Local United Engineering Laboratory of Natural Biotoxin, Fuzhou, China
- Apitherapy Research Institute of Fujian Province, Fuzhou, China
| | - Rui Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou, China
- National and Local United Engineering Laboratory of Natural Biotoxin, Fuzhou, China
- Apitherapy Research Institute of Fujian Province, Fuzhou, China
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StcU-2 Gene Mutation via CRISPR/Cas9 Leads to Misregulation of Spore-Cyst Formation in Ascosphaera apis. Microorganisms 2022; 10:microorganisms10102088. [PMID: 36296364 PMCID: PMC9607276 DOI: 10.3390/microorganisms10102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022] Open
Abstract
Ascosphaera apis is the causative agent of honey bee chalkbrood disease, and spores are the only known source of infections. Interference with sporulation is therefore a promising way to manage A. apis. The versicolorin reductase gene (StcU-2) is a ketoreductase protein related to sporulation and melanin biosynthesis. To study the StcU-2 gene in ascospore production of A. apis, CRISPR/Cas9 was used, and eight hygromycin B antibiotic-resistant transformants incorporating enhanced green fluorescent protein (EGFP) were made and analyzed. PCR amplification, gel electrophoresis, and sequence analysis were used for target gene editing analysis and verification. The CRISPR/Cas9 editing successfully knocked out the StcU-2 gene in A. apis. StcU-2 mutants had shown albino and non-functional spore-cyst development and lost effective sporulation. In conclusion, editing of StcU-2 gene has shown direct relation with sporulation and melanin biosynthesis of A. apis; this effective sporulation reduction would reduce the spread and pathogenicity of A. apis to managed honey bee. To the best of our knowledge, this is the first time CRISPR/Cas9-mediated gene editing has been efficiently performed in A. apis, a fungal honey bee brood pathogen, which offers a comprehensive set of procedural references that contributes to A. apis gene function studies and consequent control of chalkbrood disease.
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Maccaro JJ, Moreira Salgado JF, Klinger E, Argueta Guzmán MP, Ngor L, Stajich JE, McFrederick QS. Comparative genomics reveals that metabolism underlies evolution of entomopathogenicity in bee-loving Ascosphaera spp. fungi. J Invertebr Pathol 2022; 194:107804. [PMID: 35933037 PMCID: PMC10793876 DOI: 10.1016/j.jip.2022.107804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/16/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022]
Abstract
Ascosphaera (Eurotiomycetes: Onygenales) is a diverse genus of fungi that is exclusively found in association with bee nests and comprises both saprophytic and entomopathogenic species. To date, most genomic analyses have been focused on the honeybee pathogen A. apis, and we lack a genomic understanding of how pathogenesis evolved more broadly in the genus. To address this gap we sequenced the genomes of the leaf-cutting bee pathogen A. aggregata as well as three commensal species: A. pollenicola, A. atra and A. acerosa. De novo annotation and comparison of the assembled genomes was carried out, including the previously published genome of A. apis. To identify candidate virulence genes in the pathogenic species, we performed secondary metabolite-oriented analyses and clustering of biosynthetic gene clusters (BGCs). Additionally, we captured single copy orthologs to infer their phylogeny and created codon-aware alignments to determine orthologs under selective pressure in our pathogenic species. Our results show several shared BGCs between A. apis, A. aggregata and A. pollenicola, with antifungal resistance related genes present in the bee pathogens and commensals. Genes involved in metabolism and protein processing exhibit signatures of enrichment and positive selection under a fitted branch-site model. Additional known virulence genes in A. pollenicola, A. acerosa and A. atra are identified, supporting previous hypotheses that these commensals may be opportunistic pathogens. Finally, we discuss the importance of such genes in other fungal pathogens, suggesting a common route to evolution of pathogenicity in Ascosphaera.
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Affiliation(s)
- J J Maccaro
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - J F Moreira Salgado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, RJ, Brazil; Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - E Klinger
- Department of Entomology, The Ohio State University, Columbus, OH, USA; USDA-ARS Pollinating Insect Biology Management Systematics Research Unit, Logan, UT, USA
| | - M P Argueta Guzmán
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - L Ngor
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - J E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
| | - Q S McFrederick
- Department of Entomology, University of California Riverside, Riverside, CA, USA.
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Deng Y, Zhao H, Shen S, Yang S, Yang D, Deng S, Hou C. Identification of Immune Response to Sacbrood Virus Infection in Apis cerana Under Natural Condition. Front Genet 2020; 11:587509. [PMID: 33193724 PMCID: PMC7649357 DOI: 10.3389/fgene.2020.587509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/05/2020] [Indexed: 12/03/2022] Open
Abstract
Chinese sacbrood virus (CSBV) is a serious threat to eastern honeybees (Apis cerana), especially larvae. However, the pathological mechanism of this deadly disease remains unclear. Here, we employed mRNA and small RNA (sRNA) transcriptome approach to investigate the microRNAs (miRNAs) and small interfering RNAs (siRNAs) expression changes of A. cerana larvae infected with CSBV under natural condition. We found that serine proteases involved in immune response were down-regulated, while the expression of siRNAs targeted to serine proteases were up-regulated. In addition, CSBV infection also affected the expression of larvae cuticle proteins such as larval cuticle proteins A1A and A3A, resulting in increased susceptibility to CSBV infection. Together, our results provide insights into sRNAs that they are likely to be involved in regulating honeybee immune response.
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Affiliation(s)
- Yanchun Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Pollinating Insect Biology, Ministry of Agricultural and Rural Affairs, Beijing, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongxia Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, China
| | - Shuo Shen
- Qinghai Academy of Agriculture and Forestry Sciences (Academy of Agriculture and Forestry Sciences), Qinghai University, Xining, China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Pollinating Insect Biology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Dahe Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Pollinating Insect Biology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Pollinating Insect Biology, Ministry of Agricultural and Rural Affairs, Beijing, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Pollinating Insect Biology, Ministry of Agricultural and Rural Affairs, Beijing, China
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Li Z, Hou M, Qiu Y, Zhao B, Nie H, Su S. Changes in Antioxidant Enzymes Activity and Metabolomic Profiles in the Guts of Honey Bee ( Apis mellifera) Larvae Infected with Ascosphaera apis. INSECTS 2020; 11:insects11070419. [PMID: 32640515 PMCID: PMC7412215 DOI: 10.3390/insects11070419] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 01/26/2023]
Abstract
The fungus Ascosphaera apis, an obligate fungal pathogen of honey bee brood, causes chalkbrood disease in honey bee larvae worldwide. Biological characteristics of the fungal pathogen and the molecular interactions between A. apis and honey bees have been studied extensively. However, little is known about the effects of A. apis infection on antioxidant enzyme activities and metabolic profiles of the gut of honey bee larvae. In this study, sandwich enzyme-linked immunosorbent assay and LC-MS based untargeted metabolomic analysis were employed to determine the changes in the specific activities of antioxidant enzymes and the metabolomic profiles in gut tissues of A. apis-infected larvae (105 A. apis spores per larva) and controls. Results showed that specific activities of superoxide dismutase, catalase and glutathione S-transferase were significantly higher in the guts of the control larvae than in the guts of the A. apis-infected larvae. The metabolomic data revealed that levels of 28 and 52 metabolites were significantly higher and lower, respectively, in the guts of A. apis-infected larvae than in the guts of control larvae. The 5-oxo-ETE level in the infected larvae was two times higher than that in the control larvae. Elevated 5-oxo-ETE levels may act as a potential metabolic biomarker for chalkbrood disease diagnosis, suggesting that A. apis infection induced obvious oxidative stress in the honey bee larvae. The levels of metabolites such as taurine, docosahexaenoic acid, and L-carnitine involved in combating oxidative stress were significantly decreased in the gut of A. apis-infected larvae. Overall, our results suggest that A. apis infection may compromise the ability of infected larvae to cope with oxidative stress, providing new insight into changing patterns of physiological responses to A. apis infection in honey bee larvae by concurrent use of conventional biochemical assays and untargeted metabolomics.
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Getachew A, Abejew TA, Wu J, Xu J, Yu H, Tan J, Wu P, Tu Y, Kang W, Wang Z, Xu S. Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis. Sci Rep 2020; 10:7532. [PMID: 32372055 PMCID: PMC7200787 DOI: 10.1038/s41598-020-64022-3] [Citation(s) in RCA: 3] [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: 05/17/2019] [Accepted: 04/03/2020] [Indexed: 11/30/2022] Open
Abstract
Chalkbrood disease is caused by Ascosphaera apis which severely affects honeybee brood. Spore inoculation experiments shown pathogenicity varies among different strains and mutants, however, the molecular mechanism of pathogenicity is unclear. We sequenced, assembled and annotated the transcriptomes of wild type (SPE1) and three mutants (SPE2, SPE3 and SPE4) with reduced pathogenicity that were constructed in our previous study. Illumina sequencing generated a total of 394,910,604 clean reads and de novo Trinity-based assembled into 12,989 unigenes, among these, 9,598 genes were successfully annotated to known proteins in UniProt database. A total of 172, 3,996, and 650 genes were up-regulated and 4,403, 2,845, and 3,016 genes were down-regulated between SPE2-SPE1, SPE3-SPE1, and SPE4-SPE1, respectively. Overall, several genes with a potential role in fungal pathogenicity were detected down-regulated in mutants including 100 hydrolytic enzymes, 117 transcriptional factors, and 47 cell wall related genes. KEGG pathway enrichment analysis reveals 216 genes involved in nine pathways were down-regulated in mutants compared to wild type. The down-regulation of more pathways involved in pathogenicity in SPE2 and SPE4 than SPE3 supports their lower pathogenicity during in-vitro bioassay experiment. Expression of 12 down-regulated genes in mutants was validated by quantitative real time PCR. This study provides valuable information on transcriptome variation caused by mutation for further functional validation of candidate pathogenicity genes in A. apis.
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Affiliation(s)
- Awraris Getachew
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
- College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Tessema Aynalem Abejew
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
- College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Jiangli Wu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Jin Xu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Huimin Yu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Jing Tan
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Pengjie Wu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Yangyang Tu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Weipeng Kang
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Zheng Wang
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China
| | - Shufa Xu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture; Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, 100093, Beijing, China.
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Garcia Garces H, Hamae Yamauchi D, Theodoro RC, Bagagli E. PRP8 Intein in Onygenales: Distribution and Phylogenetic Aspects. Mycopathologia 2019; 185:37-49. [PMID: 31286362 DOI: 10.1007/s11046-019-00355-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022]
Abstract
Inteins (internal proteins) are mobile genetic elements, inserted in housekeeping proteins, with self-splicing properties. Some of these elements have been recently pointed out as modulators of genetic expression or protein function. Herein, we evaluated, in silico, the distribution and phylogenetic patterns of PRP8 intein among 93 fungal strains of the order Onygenales. PRP8 intein(s) are present in most of the species (45/49), mainly as full-length inteins (containing both the Splicing and the Homing Endonuclease domains), and must have transferred vertically in all lineages, since their phylogeny reflects the group phylogeny. While the distribution of PRP8 intein(s) varies among species of Onygenaceae family, being absent in Coccidioides spp. and present as full and mini-intein in other species, they are consistently observed as full-length inteins in all evaluated pathogenic species of the Arthrodermataceae and Ajellomycetaceae families. This conservative and massive PRP8 intein presence in Ajellomycetacean and Arthrodermatecean species reinforces the previous idea that such genetic elements do not decrease the fungal fitness significantly and even might play some role in the host-pathogen relationship, at least in these two fungal groups. We may better position the species Ophidiomyces ophiodiicola (with no intein) in the Onygenaceae family and Onygena corvina (with a full-length intein) as a basal member in the Arthrodermataceae family.
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Affiliation(s)
- Hans Garcia Garces
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil
| | - Danielle Hamae Yamauchi
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil
| | - Raquel Cordeiro Theodoro
- Tropical Medicine Institute of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Eduardo Bagagli
- Microbiology and Immunology Department, Biosciences Institute of Botucatu, State University of Sao Paulo (UNESP), Botucatu, São Paulo, Brazil.
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Ying SH, Feng MG. Insight into vital role of autophagy in sustaining biological control potential of fungal pathogens against pest insects and nematodes. Virulence 2018; 10:429-437. [PMID: 30257619 PMCID: PMC6550541 DOI: 10.1080/21505594.2018.1518089] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a conserved self-degradation mechanism that governs a large array of cellular processes in filamentous fungi. Filamentous insect and nematode mycopthogens function in the natural control of host populations and have been widely applied for biological control of insect and nematode pests. Entomopathogenic and nematophagous fungi have conserved “core” autophagy machineries that are analogous to those found in yeast but also feature several proteins involved in specific aspects of the autophagic pathways. Here, we review the functions of autophagy in protecting fungal cells from starvation and stress cues and sustaining cell differentiation, asexual development and virulence. An emphasis is placed upon the regulatory mechanisms involved in autophagic and non-autophagic roles of some autophagy-related genes. Methods used for monitoring conserved or specific autophagic events in fungal pathogens are also discussed.
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Affiliation(s)
- Sheng-Hua Ying
- a Institute of Microbiology, College of Life Sciences , Zhejiang University , Hangzhou , China
| | - Ming-Guang Feng
- a Institute of Microbiology, College of Life Sciences , Zhejiang University , Hangzhou , China
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Wang Z, Sun L, Guan W, Zhou C, Tang B, Cheng Y, Huang J, Xuan F. De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II). BMC Genet 2018; 19:3. [PMID: 29298661 PMCID: PMC5753516 DOI: 10.1186/s12863-017-0592-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/20/2017] [Indexed: 12/17/2022] Open
Abstract
Background The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Studies are rarely conducted on the molecular regulatory mechanism underlying the development of the reproductive system during the mating embrace stage in this species. In this study, we used high-throughput sequencing to sequence all transcriptomes of the P. trituberculatus reproductive system. Results Transcriptome sequencing of the reproductive system produced 81,688,878 raw reads (38,801,152 and 42,887,726 reads from female and male crabs, respectively). Low-quality (quality <20) reads were trimmed and removed, leaving only high-quality reads (37,020,664 and 41,021,030 from female and male crabs, respectively). A total of 126,188 (female) and 164,616 (male) transcripts were then generated by de novo transcriptome assembly using Trinity. Functional annotation of the obtained unigenes revealed that a large number of key genes and some important pathways may participate in cell proliferation and signal transduction. On the basis of our transcriptome analyses and as confirmed by quantitative real-time PCR, a number of genes potentially involved in the regulation of gonadal development and reproduction of P. trituberculatus were identified: ADRA1B, BAP1, ARL3, and TRPA1. Conclusion This study is the first to report on the whole reproductive system transcriptome information in stage II of P. trituberculatus gonadal development and provides rich resources for further studies to elucidate the molecular basis of the development of reproductive systems and reproduction in crabs. The current study can be used to further investigate functional genomics in this species. Electronic supplementary material The online version of this article (10.1186/s12863-017-0592-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Linxia Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Weibing Guan
- Key Laboratory of Shanghai Education Commission for Oceanic Fisheries Resources Exploitation, Shanghai Ocean University, Shanghai, 200090, People's Republic of China
| | - Chunlin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China
| | - Yongxu Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 200090, People's Republic of China
| | - Jintian Huang
- Yancheng Institute of Technology, Yancheng, 224051, People's Republic of China
| | - Fujun Xuan
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China. .,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 200090, People's Republic of China.
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Monteiro MC, Garcia-Rubio R, Alcazar-Fuoli L, Peláez T, Mellado E. Could the determination of Aspergillus fumigatus mating type have prognostic value in invasive aspergillosis? Mycoses 2017; 61:172-178. [PMID: 29082564 DOI: 10.1111/myc.12720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022]
Abstract
A clear link between mating type and virulence has been demonstrated for some fungal pathogens, but not for Aspergillus fumigatus as of yet. An association between mating type and invasiveness has recently been established. The mating type proportion (MAT1-1:MAT1-2) of 213 A. fumigatus strains was determined (48.5%:51.5%) and results were in agreement with previous studies. However, these percentages changed when the strain collection was divided into azole-susceptible and -resistant strains. The 163 susceptible strains kept these proportions, but among the 50 azole-resistant strains 60.0% MAT1-1 and 40% MAT1-2 were found. Moreover, looking at the clinical outcome associated to 27 azole-resistant strains, we found that MAT1-1 was linked to a high mortality rate (64%), whereas the rate associated to MAT1-2 genotype was markedly lower (15%). The pathogenicity linked to the Mat type was tested in a Galleria mellonella model of infection, showing that MAT1-1 strains were consistently more pathogenic than MAT1-2, independently of their susceptibility phenotype. This data would suggest that A. fumigatus mating type determination at the time of diagnosis could have a prognostic value in invasive aspergillosis.
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Affiliation(s)
- Maria Candida Monteiro
- Mycology Reference Laboratory, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Rocio Garcia-Rubio
- Mycology Reference Laboratory, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Alcazar-Fuoli
- Mycology Reference Laboratory, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Peláez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañon, Instituto de Investigacion Biomedica, Madrid, Spain.,Faculty of Medicine, Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Emilia Mellado
- Mycology Reference Laboratory, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
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Abstract
Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.
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Affiliation(s)
- Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77054
| | - James B Gloer
- Department of Chemistry, University of Iowa, Iowa City, IA 52245
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12
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Chou HC, Pruitt MM, Bastin BR, Schneider SQ. A transcriptional blueprint for a spiral-cleaving embryo. BMC Genomics 2016; 17:552. [PMID: 27496340 PMCID: PMC4974748 DOI: 10.1186/s12864-016-2860-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/29/2016] [Indexed: 01/29/2023] Open
Abstract
Background The spiral cleavage mode of early development is utilized in over one-third of all animal phyla and generates embryonic cells of different size, position, and fate through a conserved set of stereotypic and invariant asymmetric cell divisions. Despite the widespread use of spiral cleavage, regulatory and molecular features for any spiral-cleaving embryo are largely uncharted. To address this gap we use RNA-sequencing on the spiralian model Platynereis dumerilii to capture and quantify the first complete genome-wide transcriptional landscape of early spiral cleavage. Results RNA-sequencing datasets from seven stages in early Platynereis development, from the zygote to the protrochophore, are described here including the de novo assembly and annotation of ~17,200 Platynereis genes. Depth and quality of the RNA-sequencing datasets allow the identification of the temporal onset and level of transcription for each annotated gene, even if the expression is restricted to a single cell. Over 4000 transcripts are maternally contributed and cleared by the end of the early spiral cleavage phase. Small early waves of zygotic expression are followed by major waves of thousands of genes, demarcating the maternal to zygotic transition shortly after the completion of spiral cleavages in this annelid species. Conclusions Our comprehensive stage-specific transcriptional analysis of early embryonic stages in Platynereis elucidates the regulatory genome during early spiral embryogenesis and defines the maternal to zygotic transition in Platynereis embryos. This transcriptome assembly provides the first systems-level view of the transcriptional and regulatory landscape for a spiral-cleaving embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2860-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hsien-Chao Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Margaret M Pruitt
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: Department of Pediatrics, University of Chicago, Chicago, IL, USA
| | - Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.
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Grozinger CM, Robinson GE. The power and promise of applying genomics to honey bee health. CURRENT OPINION IN INSECT SCIENCE 2015; 10:124-132. [PMID: 26273565 PMCID: PMC4528376 DOI: 10.1016/j.cois.2015.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
New genomic tools and resources are now being used to both understand honey bee health and develop tools to better manage it. Here, we describe the use of genomic approaches to identify and characterize bee parasites and pathogens, examine interactions among these parasites and pathogens, between them and their bee hosts, and to identify genetic markers for improved breeding of more resilient bee stocks. We also discuss several new genomic techniques that can be used to more efficiently study, monitor and improve bee health. In the case of using RNAi-based technologies to mitigate diseases in bee populations, we highlight advantages, disadvantages and strategies to reduce risk. The increased use of genomic analytical tools and manipulative technologies has already led to significant advances, and holds great promise for improvements in the health of honey bees and other critical pollinator species.
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Affiliation(s)
- Christina M. Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA 16803
| | - Gene E. Robinson
- Department of Entomology, Neuroscience Program, Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 61801
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14
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Evison SE. Chalkbrood: epidemiological perspectives from the host-parasite relationship. CURRENT OPINION IN INSECT SCIENCE 2015; 10:65-70. [PMID: 29588016 DOI: 10.1016/j.cois.2015.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 06/08/2023]
Abstract
Chalkbrood is a fungal brood disease of the honey bee, Apis mellifera, caused by the parasite Ascosphaera apis. Considered as a stress-related disease, the severity of chalkbrood outbreaks depend on a multitude of interacting factors. The specific relationship between host and parasite in this disease is interesting because the parasite is both heterothallic and semelparous. Recent studies highlight that this specific host-parasite relationship is influenced by factors such as interactions with other parasite strains or species, and environmental perturbations. To understand how to protect pollinators most effectively, it is crucial that future research takes a more ecologically relevant approach by studying the basic biology of the host-parasite relationship in the context of the multi-factorial processes that influence it.
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Affiliation(s)
- Sophie Ef Evison
- Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.
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15
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Velez P, Alejandri-Ramírez ND, González MC, Estrada KJ, Sanchez-Flores A, Dinkova TD. Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions. G3 (BETHESDA, MD.) 2015; 5:1805-14. [PMID: 26116293 PMCID: PMC4555217 DOI: 10.1534/g3.115.019620] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/19/2015] [Indexed: 01/10/2023]
Abstract
Marine sandy beaches represent dynamic environments often subject to harsh conditions and climate fluctuations, where natural and anthropogenic inputs of freshwater from fluvial and pluvial sources alter salinity, which has been recognized as a key variable affecting the distribution of aquatic organisms and influencing critical physiological processes. The marine arenicolous fungus Corollospora maritima is a worldwide-distributed saprobe that has been reported to present tolerance to freshwater. Here, we present a transcriptome analysis that will provide the first insight of the genomic content for this fungus and a gene expression comparison between two different salinity conditions. We also identified genes that are candidates for being differentially expressed in response to environmental variations on salinity during the fungal growth. The de novo reconstruction of C. maritima transcriptome Illumina sequencing provided a total of 14,530 transcripts (16 megabases). The comparison between the two growth conditions rendered 103 genes specifically overexpressed in seawater, and 132 genes specifically up-regulated under freshwater. Using fungal isolates collected from different beaches, the specific environmental regulation of particular transcript differential expression was confirmed by RT-qPCR. To our knowledge, this is the first analysis that explores the marine fungus C. maritima molecular responses to overcome freshwater stress, and these data could shed light to understand the fungal adaptation and plasticity mechanisms to the marine habitat.
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Affiliation(s)
- Patricia Velez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, México 04510
| | - Naholi D Alejandri-Ramírez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Distrito Federal, México 04510
| | - María C González
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, México 04510
| | - Karel J Estrada
- Unidad de Secuenciación Masiva y Bioinformática Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Alejandro Sanchez-Flores
- Unidad de Secuenciación Masiva y Bioinformática Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 62210
| | - Tzvetanka D Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Distrito Federal, México 04510
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16
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Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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17
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The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development. Appl Microbiol Biotechnol 2014; 98:7879-92. [PMID: 24917377 DOI: 10.1007/s00253-014-5844-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
Agaricus subrufescens is one of the most important culinary-medicinal cultivable mushrooms with potentially high-added-value products and extended agronomical valorization. The development of A. subrufescens-related technologies is hampered by, among others, the lack of suitable molecular tools. Thus, this mushroom is considered as a genomic orphan species with a very limited number of available molecular markers or sequences. To fill this gap, this study reports the generation and analysis of the first set of expressed sequence tags (EST) for A. subrufescens. cDNA fragments obtained from young sporophores (SP) and vegetative mycelium in liquid culture (CL) were sequenced using 454 pyrosequencing technology. After assembly process, 4,989 and 5,125 sequences were obtained in SP and CL libraries, respectively. About 87% of the EST had significant similarity with Agaricus bisporus-predicted proteins, and 79% correspond to known proteins. Functional categorization according to Gene Ontology could be assigned to 49% of the sequences. Some gene families potentially involved in bioactive compound biosynthesis could be identified. A total of 232 simple sequence repeats (SSRs) were identified, and a set of 40 EST-SSR polymorphic markers were successfully developed. This EST dataset provides a new resource for gene discovery and molecular marker development. It constitutes a solid basis for further genetic and genomic studies in A. subrufescens.
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Giorello FM, Feijoo M, D’Elía G, Valdez L, Opazo JC, Varas V, Naya DE, Lessa EP. Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. BMC Genomics 2014; 15:446. [PMID: 24909751 PMCID: PMC4189146 DOI: 10.1186/1471-2164-15-446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/27/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption. RESULTS Transcriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models. CONCLUSION Based on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.
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Affiliation(s)
- Facundo M Giorello
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matias Feijoo
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo D’Elía
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Lourdes Valdez
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Valeria Varas
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel E Naya
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Enrique P Lessa
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
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Li Z, Su S, Hamilton M, Yan L, Chen Y. The ability to cause infection in a pathogenic fungus uncovers a new biological feature of honey bee viruses. J Invertebr Pathol 2014; 120:18-22. [PMID: 24825460 DOI: 10.1016/j.jip.2014.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/03/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
We demonstrated that honey bee viruses including Deformed wing virus (DWV), Black queen cell virus (BQCV) and Israeli acute paralysis virus (IAPV) could infect and replicate in the fungal pathogen Ascosphaera apis that causes honey bee chalkbrood disease, revealing a novel biological feature of honey bee viruses. The phylogenetic analysis show that viruses of fungal and honey bee origins form two clusters in the phylogenetic trees distinctly and that host range of honey bee viruses is dynamic. Further studies are warranted to investigate the impact of the viruses on the fitness of their fungal host and phenotypic effects the virus-fungus combination has on honey bee hosts.
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Affiliation(s)
- Zhiguo Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; USDA-ARS, Bee Research Laboratory, Beltsville, MD 20705, USA
| | - Songkun Su
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | | | - Limin Yan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yanping Chen
- USDA-ARS, Bee Research Laboratory, Beltsville, MD 20705, USA.
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De novo transcriptome hybrid assembly and validation in the European earwig (Dermaptera, Forficula auricularia). PLoS One 2014; 9:e94098. [PMID: 24722757 PMCID: PMC3983118 DOI: 10.1371/journal.pone.0094098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/10/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The European earwig (Forficula auricularia) is an established system for studies of sexual selection, social interactions and the evolution of parental care. Despite its scientific interest, little knowledge exists about the species at the genomic level, limiting the scope of molecular studies and expression analyses of genes of interest. To overcome these limitations, we sequenced and validated the transcriptome of the European earwig. METHODOLOGY AND PRINCIPAL FINDINGS To obtain a comprehensive transcriptome, we sequenced mRNA from various tissues and developmental stages of female and male earwigs using Roche 454 pyrosequencing and Illumina HiSeq. The reads were de novo assembled independently and screened for possible microbial contamination and repeated elements. The remaining contigs were combined into a hybrid assembly and clustered to reduce redundancy. A comparison with the eukaryotic core gene dataset indicates that we sequenced a substantial part of the earwig transcriptome with a low level of fragmentation. In addition, a comparative analysis revealed that more than 8,800 contigs of the hybrid assembly show significant similarity to insect-specific proteins and those were assigned for Gene Ontology terms. Finally, we established a quantitative PCR test for expression stability using commonly used housekeeping genes and applied the method to five homologs of known sex-biased genes of the honeybee. The qPCR pilot study confirmed sex specific expression and also revealed significant expression differences between the brain and antenna tissue samples. CONCLUSIONS By employing two different sequencing approaches and including samples obtained from different tissues, developmental stages, and sexes, we were able to assemble a comprehensive transcriptome of F. auricularia. The transcriptome presented here offers new opportunities to study the molecular bases and evolution of parental care and sociality in arthropods.
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