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Hanada T, Yaguchi H, Fujiwara K, Hayashi Y, Nalepa CA, Maekawa K. Differential Expression of Hormone-Related Genes in the Heads of Adult and Nymphal Woodroaches (Cryptocercus). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2025; 344:182-197. [PMID: 39959923 DOI: 10.1002/jez.b.23290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 12/26/2024] [Accepted: 01/29/2025] [Indexed: 05/03/2025]
Abstract
Termites are eusocial cockroaches, but the crucial distinctions in gene expression during the evolution of eusociality remain unclear. One reason for the lack of this information is that comparative transcriptome analysis of termites with their sister group, the cockroach genus Cryptocercus, has not been conducted. We identified genes associated with three vital hormones (juvenile hormone [JH], 20-hydoroxyecdysone [20E], and insulin) from the genome sequence of Cryptocercus punctulatus and conducted RNA-seq analysis using the heads of female/male adults and nymphs to elucidate their expression levels. The comprehensive gene expression analysis revealed a multitude of genes exhibiting differences in expression between developmental stages rather than between sexes. Subsequently, we compared the differences in expression patterns of each hormone-related gene by combining the results of a previous RNA-seq study conducted on the heads of castes (reproductives, workers, and soldiers) in the termite Reticulitermes speratus. The results indicated that genes with expression differences among castes in R. speratus, particularly those related to JH and 20E, were significantly more abundant compared to genes with expression differences between adults and nymphs in C. punctulatus. While no significant difference was observed in the number of genes within the insulin signaling pathway, a trend of homologs highly expressed in adult woodroaches but not in adult termites was observed, and the expression patterns of positive and negative regulators in the pathway differed significantly between adults and nymphs. The differences in the expression patterns between Cryptocercus and termites are believed to reflect variations in hormone levels and signaling activities between adults and juveniles, the latter encompassing workers and soldiers in the case of termites.
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Affiliation(s)
- Takumi Hanada
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Hajime Yaguchi
- Department of Forest Entomology, Forestry and Forest Products Research Institute, Tsukuba, Japan
| | - Kokuto Fujiwara
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | | | - Christine A Nalepa
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
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2
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He B, Cong Y, Xu L, Liu Y. Expansion of three types of transposon superfamilies within 25 Mya lead to large genome size of a rice insect pest. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2025; 177:104251. [PMID: 39694421 DOI: 10.1016/j.ibmb.2024.104251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 10/18/2024] [Accepted: 12/15/2024] [Indexed: 12/20/2024]
Abstract
The brown planthoppers (BPH, Nilaparvata lugens), white backed planthopper (WBPH, Sogatella furcifera) and small brown planthopper (SBPH, Laodelphax striatellus) are widely distributed rice insect pests, causing huge annual yield loss of rice production. Though these three planthoppers belong to the same family, Delphacidae of Hemiptera, their genome sizes (GS) are very different, ranging from 541 to 1088 Mb. To uncover the main factors driving GS changes of three planthoppers, we first estimated the GS of their ancestor Fulgoroidea, to be 794.33 Mb, indicating GS expansion in BPH but contraction in SBPH and WBPH. Next, we identified repetitive sequences and compared the TE landscapes, showed that three types of transposon superfamilies, hAT, Tc1-Mariner and Gypsy, expanded within 25 Mya in BPH. In addition, BPH kept ancient TEs of Fulgoroidea dated back to 175 Mya, while SBPH and WBPH have lost most of these ancient TEs. Here, we present evidence that the gain of recently expanded TEs driving the GS expansion and loss of ancient TEs leading to the GS contraction, providing new insights into the mechanism of GS variation.
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Affiliation(s)
- Bingbing He
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China; State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Le Xu
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
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3
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Martelossi J, Forni G, Iannello M, Savojardo C, Martelli PL, Casadio R, Mantovani B, Luchetti A, Rota-Stabelli O. Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae). INSECT MOLECULAR BIOLOGY 2023; 32:118-131. [PMID: 36366787 DOI: 10.1111/imb.12818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Termites (Insecta, Blattodea, Termitoidae) are a widespread and diverse group of eusocial insects known for their ability to digest wood matter. Herein, we report the draft genome of the subterranean termite Reticulitermes lucifugus, an economically important species and among the most studied taxa with respect to eusocial organization and mating system. The final assembly (~813 Mb) covered up to 88% of the estimated genome size and, in agreement with the Asexual Queen Succession Mating System, it was found completely homozygous. We predicted 16,349 highly supported gene models and 42% of repetitive DNA content. Transposable elements of R. lucifugus show similar evolutionary dynamics compared to that of other termites, with two main peaks of activity localized at 25% and 8% of Kimura divergence driven by DNA, LINE and SINE elements. Gene family turnover analyses identified multiple instances of gene duplication associated with R. lucifugus diversification, with significant lineage-specific gene family expansions related to development, perception and nutrient metabolism pathways. Finally, we analysed P450 and odourant receptor gene repertoires in detail, highlighting the large diversity and dynamical evolutionary history of these proteins in the R. lucifugus genome. This newly assembled genome will provide a valuable resource for further understanding the molecular basis of termites biology as well as for pest control.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment C3A, University of Trento/Fondazione Edmund Mach, Trento, Italy
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4
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Liu X, Majid M, Yuan H, Chang H, Zhao L, Nie Y, He L, Liu X, He X, Huang Y. Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism. BMC Biol 2022; 20:243. [PMID: 36307800 PMCID: PMC9615261 DOI: 10.1186/s12915-022-01441-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs.
Results
We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level.
Conclusions
Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.
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Cong Y, Ye X, Mei Y, He K, Li F. Transposons and non-coding regions drive the intrafamily differences of genome size in insects. iScience 2022; 25:104873. [PMID: 36039293 PMCID: PMC9418806 DOI: 10.1016/j.isci.2022.104873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein-Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.
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Affiliation(s)
- Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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6
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Using ultraconserved elements to reconstruct the termite tree of life. Mol Phylogenet Evol 2022; 173:107520. [DOI: 10.1016/j.ympev.2022.107520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
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7
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Maekawa K, Hayashi Y, Lo N. Termite sociogenomics: evolution and regulation of caste-specific expressed genes. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100880. [PMID: 35123120 DOI: 10.1016/j.cois.2022.100880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/12/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Termite genomes have been sequenced in at least five species from four different families. Genome-based transcriptome analyses have identified large numbers of protein-coding genes with caste-specific expression patterns. These genes include those involved in caste-specific morphologies and roles, for example high fecundity and longevity in reproductives. Some caste-specific expressed genes belong to multi-gene families, and their genetic architecture and expression profiles indicate they have evolved via tandem gene duplication. Candidate regulatory mechanisms of caste-specific expression include epigenetic regulation (e.g. histone modification and non-coding RNA) and diversification of transcription factors and cis-regulatory elements. We review current knowledge in the area of termite sociogenomics, focussing on the evolution and regulation of caste-specific expressed genes, and discuss future research directions.
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Affiliation(s)
- Kiyoto Maekawa
- Faculty of Science, Academic Assembly, University of Toyama, Toyama, Japan
| | - Yoshinobu Hayashi
- Department of Biology, Keio University, Hiyoshi, Yokohama 223-8521, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, NSW, Australia
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8
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Monti M, Redi C, Capanna E. Genome size evaluations in cockroaches: new entries. Eur J Histochem 2022; 66. [PMID: 35332752 PMCID: PMC8992379 DOI: 10.4081/ejh.2022.3400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
In this paper, we report genome size (GS) values for nine cockroaches (order Blattodea, families Blattidae, Blaberidae and Ectobiidae, ex Blattelidae), three of which are original additions to the ten already present in the GS database: the death’s head roach (Blaberus craniifer), the Surinam cockroach (Pycnoscelus surinamensis) and the Madeira cockroach (Leucophaea maderae). Regarding the American cockroach (Periplaneta americana), the GS database contains two contrasting values (2.72 vs 3.41 pg); likely, the 2.72 pg value is the correct one as it is strikingly similar to our sperm DNA content evaluation (2.80 ± 0.11 pg). Also, we suggest halving the published GS of the Argentine cockroach Blaptica dubia and the spotted cockroach (the gray cockroach) Nauphoeta cinerea discussing i) the occurrence of a correlation between increasing 2n chromosome number and GS within the order Blattodea; and ii) the possible occurrence of a polyploidization phenomenon doubling a basic GS of 0.58 pg of some termite families (superfamily Blattoidea, epifamily Termitoidae).
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Affiliation(s)
- Manuela Monti
- Department of Public Health, Experimental and Forensic Medicine, Histology and Embryology Unit, University of Pavia.
| | - CarloAlberto Redi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia.
| | - Ernesto Capanna
- Department of Animal Biology "Agostino Bassi", "La Sapienza" University of Rome.
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9
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Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proc Natl Acad Sci U S A 2022; 119:2110361119. [PMID: 35042774 PMCID: PMC8785959 DOI: 10.1073/pnas.2110361119] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
Gene duplication is a major source of evolutionary innovation and is associated with the increases in biological complexity and adaptive radiation. Termites are model social organisms characterized by a sophisticated caste system. We analyzed the genome of the Japanese subterranean termite, an ecologically and economically important insect acting as a destructive pest. The analyses revealed the significance of gene duplication in social evolution. Gene duplication associated with caste-biased gene expression was prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity, and defense, and they were often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome, and methylome of the Japanese subterranean termite Reticulitermes speratus. Our analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression was prevalent in the R. speratus genome. The duplicated genes comprised diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense), and a novel class of termite lineage–specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but their expression patterns were highly variable, exhibiting caste biases. Some of the assayed duplicated genes were expressed in caste-specific organs, such as the accessory glands of the queen ovary and the frontal glands of soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization conferring caste-specialized functions.
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10
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Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci U S A 2021; 118:e2025051118. [PMID: 34099551 PMCID: PMC8214670 DOI: 10.1073/pnas.2025051118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027;
- Department of Biological Sciences, State University of New York College at Old Westbury, Old Westbury, NY 11568
| | - Stephen E Harris
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
- Department of Biology, State University of New York Purchase College, Purchase, NY 10577
| | | | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS B2Y 4A2, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dustin R Rubenstein
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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11
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Hussin NA, Najimudin N, Ab Majid AH. The de novo transcriptome of workers head of the higher group termite Globitermes sulphureus Haviland (Blattodea: Termitidae). Heliyon 2019; 5:e02969. [PMID: 31872129 PMCID: PMC6909072 DOI: 10.1016/j.heliyon.2019.e02969] [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: 06/28/2019] [Revised: 11/04/2019] [Accepted: 11/28/2019] [Indexed: 11/26/2022] Open
Abstract
The subterranean termite Globitermus sulphureus is an important Southeast Asian pest with limited genomic resources that causes damages to agriculture crops and building structures. Therefore, the main goal of this study was to survey the G. sulphureus transcriptome composition. Here, we performed de novo transcriptome for G. sulphureus workers’ heads using Illumina HiSeq paired-end sequencing technology. A total of 88, 639, 408 clean reads were collected and assembled into 243, 057 transcripts and 193, 344 putative genes. The transcripts were annotated with the Trinotate pipeline. In total, 27, 061 transcripts were successfully annotated using BLASTX against the SwissProt database and 17, 816 genes were assigned to 47, 598 GO terms. We classified 14, 223 transcripts into COG classification, resulting in 25 groups of functional annotations. Next, a total of 12, 194 genes were matched in the KEGG pathway and 392 metabolic pathways were predicted based on the annotation. Moreover, we detected two endogenous cellulases in the sequences. The RT-qPCR analysis showed that there were significant differences in the expression levels of two genes β-glucosidase and endo-β-1,4-glucanase between worker and soldier heads of G. sulphureus. This is the first study to characterize the complete head transcriptome of a higher termite G. sulphureus using a high-throughput sequencing. Our study may provide an overview and comprehensive molecular resource for comparative studies of the transcriptomics and genomics of termites.
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Affiliation(s)
- Nurul Akmar Hussin
- Household and Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Abdul Hafiz Ab Majid
- Household and Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
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12
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The relationship between genome size, morphological parameters and diet breadth in insect species. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Segatto ALA, Diesel JF, Loreto ELS, da Rocha JBT. De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae). Genet Mol Biol 2018; 41:713-721. [PMID: 30043835 PMCID: PMC6136372 DOI: 10.1590/1678-4685-gmb-2017-0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/03/2018] [Indexed: 12/17/2022] Open
Abstract
The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.
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Affiliation(s)
- Ana Lúcia Anversa Segatto
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - José Francisco Diesel
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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14
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Lo N, Simpson SJ, Sword GA. Epigenetics and developmental plasticity in orthopteroid insects. CURRENT OPINION IN INSECT SCIENCE 2018; 25:25-34. [PMID: 29602359 DOI: 10.1016/j.cois.2017.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/26/2017] [Accepted: 11/06/2017] [Indexed: 06/08/2023]
Abstract
Developmental plasticity is a key driver of the extraordinary ecological success of insects. Epigenetic mechanisms provide an important link between the external stimuli that initiate polyphenisms, and the stable changes in gene expression that govern alternative insect morphs. We review the epigenetics of orthopteroid insects, focussing on recent research on locusts and termites, two groups which display high levels of phenotypic plasticity, and for which genome sequences have become available in recent years. We examine research on the potential role of DNA methylation, histone modifications, and non-coding RNAs in the regulation of gene expression in these insects. DNA methylation patterns in orthopteroids share a number of characteristics with those of hymenopteran insects, although methylation levels are much higher, and extend to introns and repeat elements. Future examinations of epigenetic mechanisms in these insects will benefit from comparison of tissues from aged-matched individuals from alternative morphs, and adequate biological replication.
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Affiliation(s)
- Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen J Simpson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory A Sword
- Department of Entomology, Interdisciplinary Faculty of Ecology and Evolutionary Biology, Texas A&M University, TAMU 2475, College Station, TX 77843, USA
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15
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Fukutomi Y, Matsumoto K, Funayama N, Koshikawa S. Methods for Staging Pupal Periods and Measurement of Wing Pigmentation of Drosophila guttifera. J Vis Exp 2018. [PMID: 29443109 DOI: 10.3791/56935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Diversified species of Drosophila (fruit fly) provide opportunities to study mechanisms of development and genetic changes responsible for evolutionary changes. In particular, the adult stage is a rich source of morphological traits for interspecific comparison, including wing pigmentation comparison. To study developmental differences among species, detailed observation and appropriate staging are required for precise comparison. Here we describe protocols for staging of pupal periods and quantification of wing pigmentation in a polka-dotted fruit fly, Drosophila guttifera. First, we describe the method for detailed morphological observation and definition of pupal stages based on morphologies. This method includes a technique for removing the puparium, which is the outer chitinous case of the pupa, to enable detailed observation of pupal morphologies. Second, we describe the method for measuring the duration of defined pupal stages. Finally, we describe the method for quantification of wing pigmentation based on image analysis using digital images and ImageJ software. With these methods, we can establish a solid basis for comparing developmental processes of adult traits during pupal stages.
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Affiliation(s)
| | - Keiji Matsumoto
- Graduate School of Science, Kyoto University; Graduate School of Science, Osaka City University
| | | | - Shigeyuki Koshikawa
- Graduate School of Science, Kyoto University; The Hakubi Center for Advanced Research, Kyoto University; Graduate School of Environmental Science, Hokkaido University;
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16
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Wu T, Dhami GK, Thompson GJ. Soldier‐biased gene expression in a subterranean termite implies functional specialization of the defensive caste. Evol Dev 2017; 20:3-16. [DOI: 10.1111/ede.12243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tian Wu
- Biology DepartmentWestern UniversityLondonOntarioCanada
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17
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Liu GC, Dong ZW, He JW, Zhao RP, Wang W, Li XY. Genome size of 14 species of fireflies (Insecta, Coleoptera, Lampyridae). Zool Res 2017; 38:449-458. [PMID: 29280364 PMCID: PMC5767557 DOI: 10.24272/j.issn.2095-8137.2017.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies (Lampyridae) (two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis) were estimated by propidium iodide (PI)-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0. 42 to 1. 31 pg, a 3. 1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.
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Affiliation(s)
- Gui-Chun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China
| | - Zhi-Wei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jin-Wu He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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18
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. Polymerase chain reaction with nearby primers. Anal Biochem 2016; 518:126-133. [PMID: 27908595 DOI: 10.1016/j.ab.2016.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023]
Abstract
DNA analysis of biological specimens containing degraded nucleic acids such as mortal remains, archaeological artefacts, forensic samples etc. has gained more attention in recent years. DNA extracted from these samples is often inapplicable for conventional polymerase chain reaction (PCR), so for its amplification the nearby primers are commonly used. Here we report the data that clarify the features of PCR with nearby and abutting primers. We have shown that the proximity of primers leads to significant reduction of the reaction time and ensures the successful performance of DNA amplification even in the presence of PCR inhibitors. The PCR with abutting primers is usually characterized by the absence of nonspecific amplification products that causes extreme sensitivity with limit of detection on single copy level. The feasibility of PCR with abutting primers was demonstrated on species identification of 100 years old rotten wood.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Aizilya A Galimova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
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19
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Burford Reiskind MO, Coyle K, Daniels HV, Labadie P, Reiskind MH, Roberts NB, Roberts RB, Schaff J, Vargo EL. Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa. Mol Ecol Resour 2016; 16:1303-1314. [PMID: 27739656 DOI: 10.1111/1755-0998.12527] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 11/28/2022]
Abstract
The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.
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Affiliation(s)
- M O Burford Reiskind
- Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA.
| | - K Coyle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - H V Daniels
- Department of Applied Ecology, North Carolina State University, Campus Box 7617, Raleigh, NC, 27695, USA
| | - P Labadie
- Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA
| | - M H Reiskind
- Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA
| | - N B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - R B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Schaff
- Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, 27695, USA
| | - E L Vargo
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
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20
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR, Chemeris AV. PCR-based evaluation of sequence specificity of DNA fragmentation by ultrasound. Mol Biol 2016. [DOI: 10.1134/s0026893316020059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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22
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR, Vakhitov VA, Chemeris AV. DNA amplification using PCR with abutting primers. Mol Biol 2015. [DOI: 10.1134/s0026893315040056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Guo LT, Wang SL, Wu QJ, Zhou XG, Xie W, Zhang YJ. Flow cytometry and K-mer analysis estimates of the genome sizes of Bemisia tabaci B and Q (Hemiptera: Aleyrodidae). Front Physiol 2015; 6:144. [PMID: 26042041 PMCID: PMC4436570 DOI: 10.3389/fphys.2015.00144] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
The genome sizes of the B- and Q-types of the whitefly Bemisia tabaci (Gennnadius) were estimated using flow cytometry (Drosophila melanogaster as the DNA reference standard and propidium iodide (PI) as the fluorochrome) and k-mer analysis. For flow cytometry, the mean nuclear DNA content was 0.686 pg for B-type males, 1.392 pg for B-type females, 0.680 pg for Q-type males, and 1.306 pg for Q-type females. Based on the relationship between DNA content and genome size (1 pg DNA = 980 Mbp), the haploid genome size of B. tabaci ranged from 640 to 682 Mbp. For k-mer analysis, genome size of B-type by two methods were consistent highly, but the k-mer depth distribution graph of Q-type was not enough perfect and the genome size was estimated about 60 M larger than its flow cytometry result. These results corroborate previous reports of genome size based on karyotype analysis and chromosome counting. However, these estimates differ from previous flow cytometry estimates, probably because of differences in the DNA reference standard and dyeing time, which were superior in the current study. For Q-type genome size difference by two method, some discussion were also stated, and all these results represent a useful foundation for B. tabaci genomics research.
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Affiliation(s)
- Li T. Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shao L. Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qing J. Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xu G. Zhou
- Department of Entomology, Agricultural Science Center North, University of KentuckyLexington, KY, USA
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - You J. Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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24
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Scharf ME. Omic research in termites: an overview and a roadmap. Front Genet 2015; 6:76. [PMID: 25821456 PMCID: PMC4358217 DOI: 10.3389/fgene.2015.00076] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/13/2015] [Indexed: 11/13/2022] Open
Abstract
Many recent breakthroughs in our understanding of termite biology have been facilitated by "omics" research. Omic science seeks to collectively catalog, quantify, and characterize pools of biological molecules that translate into structure, function, and life processes of an organism. Biological molecules in this context include genomic DNA, messenger RNA, proteins, and other biochemicals. Other permutations of omics that apply to termites include sociogenomics, which seeks to define social life in molecular terms (e.g., behavior, sociality, physiology, symbiosis, etc.) and digestomics, which seeks to define the collective pool of host and symbiont genes that collaborate to achieve high-efficiency lignocellulose digestion in the termite gut. This review covers a wide spectrum of termite omic studies from the past 15 years. Topics covered include a summary of terminology, the various kinds of omic efforts that have been undertaken, what has been revealed, and to a degree, what the results mean. Although recent omic efforts have contributed to a better understanding of many facets of termite and symbiont biology, and have created important new resources for many species, significant knowledge gaps still remain. Crossing these gaps can best be done by applying new omic resources within multi-dimensional (i.e., functional, translational, and applied) research programs.
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Affiliation(s)
- Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, IN USA
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25
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Korb J, Poulsen M, Hu H, Li C, Boomsma JJ, Zhang G, Liebig J. A genomic comparison of two termites with different social complexity. Front Genet 2015; 6:9. [PMID: 25788900 PMCID: PMC4348803 DOI: 10.3389/fgene.2015.00009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/09/2015] [Indexed: 11/15/2022] Open
Abstract
The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity spectrum. Zootermopsis nevadensis has simple colonies with totipotent workers that can develop into all castes (dispersing reproductives, nest-inheriting replacement reproductives, and soldiers). In contrast, the fungus-growing termite Macrotermes natalensis belongs to the higher termites and has very large and complex societies with morphologically distinct castes that are life-time sterile. Here we compare key characteristics of genomic architecture, focusing on genes involved in communication, immune defenses, mating biology and symbiosis that were likely important in termite social evolution. We discuss these in relation to what is known about these genes in the ants and outline hypothesis for further testing.
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Affiliation(s)
- Judith Korb
- Department of Evolutionary Biology and Ecology, Institute of Biology I, University of FreiburgFreiburg, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
| | - Haofu Hu
- China National Genebank, BGI-ShenzhenShenzhen, China
| | - Cai Li
- China National Genebank, BGI-ShenzhenShenzhen, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | - Jacobus J. Boomsma
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
- China National Genebank, BGI-ShenzhenShenzhen, China
| | - Jürgen Liebig
- School of Life Sciences, Arizona State UniversityTempe, AZ, USA
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26
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Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SMS, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MAD, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J. Molecular traces of alternative social organization in a termite genome. Nat Commun 2014; 5:3636. [PMID: 24845553 DOI: 10.1038/ncomms4636] [Citation(s) in RCA: 277] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 03/13/2014] [Indexed: 01/28/2023] Open
Abstract
Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.
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Affiliation(s)
- Nicolas Terrapon
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2] [3]
| | - Cai Li
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark [3]
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lu Ji
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xuehong Meng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Warren Booth
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2]
| | - Zhensheng Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kaustubh Gokhale
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Johannes Gowin
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Wulfila Gronenberg
- Department of Neuroscience, University of Arizona, Tucson, Arizona 85721, USA
| | - Russell A Hermansen
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - Haofu Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brendan G Hunt
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA [2]
| | - Ann Kathrin Huylmans
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2]
| | - Sayed M S Khalil
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2] Department of Microbial Molecular Biology, Agricultural Genetic Engineering Research Institute, Giza 12619, Egypt
| | - Robert D Mitchell
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Monica C Munoz-Torres
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Julie A Mustard
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hailin Pan
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Justin T Reese
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Fengming Sun
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhikai Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zuoquan Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiajian Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiwei Zhu
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Colin S Brent
- Arid Land Agricultural Research Center, United States Department of Agriculture, Maricopa, Arizona 85138, USA
| | - Christine G Elsik
- 1] Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA [2] Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | | | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - R Michael Roe
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Edward L Vargo
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Andreas Vilcinskas
- Institut für Phytopathologie und Angewandte Zoologie, Justus-Liebig-Universität Giessen, Giessen D35390, Germany
| | - Jun Wang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Copenhagen DK-1165, Denmark [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, 21589 Jeddah, Saudi Arabia [4] Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China [5] Department of Medicine, University of Hong Kong, Hong Kong
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany
| | - Judith Korb
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Guojie Zhang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
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Cardoso DC, Carvalho CR, Cristiano MP, Soares FAF, Tavares MG. Estimation of nuclear genome size of the genus Mycetophylax Emery, 1913: evidence of no whole-genome duplication in Neoattini. C R Biol 2012. [PMID: 23199629 DOI: 10.1016/j.crvi.2012.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genome size estimates and their evolution can be useful for studying the phylogenetic relationships and taxonomy of a particular group. In the present study, the genome sizes of the three species that comprise the Mycetophylax genus were estimated by flow cytometry (FCM). There was little variation in genome size among them. The mean haploid genome size value of male and female individuals of Mycetophylax morschi was 312.96 Mbp (0.32 pg) and that of Mycetophylax conformis and Mycetophylax simplex females were 312.96 Mbp (0.32 pg) and 381.42 Mbp (0.39 pg), respectively. At first glance, this variation could be related with the heterochromatin content. Our results, together with other previous reports, have contributed to our knowledge about Attini genome size and will be useful to improve the understanding of the evolution of this tribe. It will help select potential model species in Attini for future genomic and sequencing projects.
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Affiliation(s)
- Danon Clemes Cardoso
- Programa de Pós-graduação em Genética e Melhoramento, Departamento de Biologia Geral, Universidade Federal de Viçosa, Avenue Peter Henry Rolfs, s.n., Minas Gerais, Brazil.
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Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome. Mol Genet Genomics 2010; 285:175-84. [PMID: 21184097 DOI: 10.1007/s00438-010-0595-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/06/2010] [Indexed: 10/18/2022]
Abstract
Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 10(3) to 10(5) copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites' SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.
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Ardila-Garcia AM, Umphrey GJ, Gregory TR. An expansion of the genome size dataset for the insect order Hymenoptera, with a first test of parasitism and eusociality as possible constraints. INSECT MOLECULAR BIOLOGY 2010; 19:337-46. [PMID: 20201980 DOI: 10.1111/j.1365-2583.2010.00992.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Although the Hymenoptera represent a remarkably diverse and socioeconomically important group that is of considerable interest in genome biology, they remain understudied in terms of genome size. This study reports new genome size estimates for 89 species of ants, bees and wasps, representing 17 families and four superfamilies. These are used in a test of the hypothesis that genome sizes are constrained by traits associated with parasitism or eusociality. Not all parasitoid wasps exhibit small genomes, though a relationship based on specific types of parasitism may still occur; by contrast, there was no convincing evidence of a constraint relating to eusociality. The data provided here can be used to guide future research aimed at understanding the evolution of large-scale genomic properties in this order.
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Affiliation(s)
- A M Ardila-Garcia
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Nakabachi A, Koshikawa S, Miura T, Miyagishima S. Genome size of Pachypsylla venusta (Hemiptera: Psyllidae) and the ploidy of its bacteriocyte, the symbiotic host cell that harbors intracellular mutualistic bacteria with the smallest cellular genome. BULLETIN OF ENTOMOLOGICAL RESEARCH 2010; 100:27-33. [PMID: 19302725 DOI: 10.1017/s0007485309006737] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Psyllids harbor the primary symbiont, Carsonella ruddii (gamma-Proteobacteria), within the cytoplasm of specialized cells called bacteriocytes. Carsonella has the smallest known cellular genome (160 kb), lacking numerous genes that appear to be essential for bacterial life. This raises the question regarding the genetic mechanisms of the host which supports the survival of Carsonella. Our preceding analyses have indicated that some of the genes that are encoded in the psyllid genome and which are highly expressed in the bacteriocyte are of bacterial origin. This implies that psyllids acquired genes from bacteria by lateral gene transfer (LGT) and are using these genes to maintain the primary symbiont, Carsonella. To reveal the complete picture of LGT from symbiotic bacteria to the genome of psyllids, whole genome analysis of psyllids is essential. In order to assess the feasibility of whole genome analysis of the host psyllid, the genome size of the hackberry petiole gall psyllid, Pachypsylla venusta, was estimated. Feulgen image analysis densitometry and flow cytometry demonstrated that the haploid genome size of P. venusta is 0.74 pg (724 Mb), verifying the feasibility of whole genome analysis. Feulgen image analysis densitometry further revealed that bacteriocytes of P. venusta are invariably 16-ploid. This higher ploidy may be essential to facilitate the symbiotic relationship with bacteria, as it appears to be a feature common to insect bacteriocytes. These results provide a foundation for genomics-based research into host-symbiont interactions.
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Affiliation(s)
- A Nakabachi
- Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Luchetti A, Mantovani B. Talua SINE Biology in the Genome of the Reticulitermes Subterranean Termites (Isoptera, Rhinotermitidae). J Mol Evol 2009; 69:589-600. [DOI: 10.1007/s00239-009-9285-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
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