1
|
Dionisio JF, Pezenti LF, de Souza RF, Sosa-Gómez DR, da Rosa R. Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution. Mol Genet Genomics 2023; 298:1377-1388. [PMID: 37646857 DOI: 10.1007/s00438-023-02063-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Transposable elements (TEs) are DNA sequences capable of moving within the genome. Their distribution is very dynamic among organisms, and despite advances, there are still gaps in the understanding of the diversity and evolution of TEs in many insect species. In the case of Euschistus heros, considered the main stink bug in the soybean crop in Brazil, little is known about the participation of these elements. Therefore, the objective of the current work was to identify the different groups of transposable elements present in the E. heros transcriptome, evidencing their chromosomal distribution. Through RNA-Seq and de novo assembly, 60,009 transcripts were obtained, which were annotated locally via Blastn against specific databases. Of the 367 transcripts identified as TEs, 202 belong to Class II, with emphasis on the TIR order. Among Class I elements or retrotransposons, most were characterized as LINE. Phylogenetic analyses were performed with the protein domains, evidencing differences between Tc1-mariner sequences, which may be related to possible horizontal transfer events. The transposable elements that stood out in the transcriptome were selected for fluorescent in situ hybridization. DNA transposon probes hAT, Helitron, and Tc1-mariner showed mostly scattered signals, with the presence of some blocks. Retrotransposon probes Copia, Gypsy, Jockey, and RTE showed a more pulverized hybridization pattern, with the presence of small interstitial and/or terminal blocks. Studies like this one, integrating functional genomics and molecular cytogenetic tools, are essential to expanding knowledge about transcriptionally active mobile elements, and their behavior in the chromosomes.
Collapse
Affiliation(s)
- Jaqueline Fernanda Dionisio
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Larissa Forim Pezenti
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Caixa Postal: 4006, Londrina, PR, CEP: 86085-981, Brazil
| | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil.
| |
Collapse
|
2
|
Lopes TBF, Aguiar RCM, de Souza RF, Nascimento CC, Dionísio JF, Mantovani MS, Semprebon SC, da Rosa R. Influence of temperature variation on gene expression and cocoon production in Bombyx mori Linnaeus, 1758 (Lepidoptera: Bombycidae). Comp Biochem Physiol Part D Genomics Proteomics 2023; 47:101111. [PMID: 37516100 DOI: 10.1016/j.cbd.2023.101111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Silkworms (Bombyx mori) are lepidopterans of economic importance for global silk production. However, factors that directly affect the yield and quality of silkworm cocoon production, such as diseases and temperature fluctuations, cause great economic losses. Knowing how they respond to rearing temperature during the most critical stage of their life cycle (i.e., fifth instar) could provide information on their adaptation and improve silk production. In the current work, we analyzed transcriptional data from two groups of B. mori that were reared at 26 °C and 34 °C throughout the fifth instar. The silkworms and cocoons were weighed. In total, 3115 transcripts were differentially expressed (DE; including 1696 down-regulated and 1419 up-regulated) among the 29,157 sequences found by transcriptome assembly. We emphasize the genes associated with immunological response, transcription factors, silk biosynthesis, and heat shock proteins, among the DE transcripts in response to the temperature conditions. Silkworms reared at 34 °C presented a reduced mean body weight (-0.944 g in comparison to the 26 °C group), which had a direct impact on the weight of cocoons formed and the silk conversion rate. These changes were statistically significant when compared to silkworms reared at 26 °C. Mortality rates (6 and 9 %, at 26 °C and 34 °C, respectively) were similar to those obtained in breeding fields. The findings provide information on the biological processes involved in the temperature response mechanism of silkworms, as well as information that may be used in future climatization processes at rearing facilities and in breeding for improved thermotolerance.
Collapse
Affiliation(s)
- Thayná Bisson Ferraz Lopes
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Rachel Colauto Milanezi Aguiar
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Cristianne Cordeiro Nascimento
- Departamento de Design Gráfico, Centro de Educação, Comunicação e Artes, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Jaqueline Fernanda Dionísio
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Mario Sergio Mantovani
- Laboratório de Genética Toxicológica, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Simone Cristine Semprebon
- Laboratório de Genética Toxicológica, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| |
Collapse
|
3
|
Pezenti LF, Dionisio JF, Sosa-Gómez DR, de Souza RF, da Rosa R. Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Genome 2023. [DOI: 10.1139/gen-2022-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis ( Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.
Collapse
|
4
|
Dias FC, de Souza RF, Pezenti LF, Dionisio JF, Paulino JAM, da Silva CRM, Sosa-Gómez DR, da Rosa R. Transcriptional Analysis of Microsatellites in Velvetbean Caterpillar Anticarsia gemmatalis Hübner, 1818. Cytogenet Genome Res 2023; 162:273-282. [PMID: 36689934 DOI: 10.1159/000527049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/14/2022] [Indexed: 01/24/2023] Open
Abstract
Brazil is the largest producer of soybeans in the world. The vast extent of soybean plantations across the Brazilian territory exposes this crop to attack by several insects, including the velvetbean caterpillar, Anticarsia gemmatalis. One of the alternatives used to control this insect are the toxins produced by Bacillus thuringiensis (Bt). However, in some cases, resistance to these toxins has been reported in the laboratory. Despite the ecological and economic impact of the velvetbean caterpillar, there are few studies on the genetic structure of this species, especially with regard to microsatellites. In this paper, we carried out a comparative transcriptional analysis of microsatellites in resistant (RES) and susceptible (SUS) strains of A. gemmatalis challenged and not challenged with Bt toxins. According to the number of sequences analyzed in each group, a 7.9% simple sequence repeat (SSR) rate was identified for the SUS library, and 7.4% for SUSBt. For the RES group, this value was 8.5% and for the RESBt 7.7%. Most of the fragments found showed a shorter repeat pattern, located in mono- and trinucleotide motifs. Among the 128 types of SSR motifs, it was possible to notice a large amount of adenine and thymine in relation to guanine and cytosine, which was also seen in chromosomes after staining with base-specific fluorochromes DAPI/CMA3, highlighting DAPI-positive regions. Although the participation of microsatellites in the resistance mechanism of A. gemmatalis to Bt is not clear, the results obtained in this work contribute to a better understanding of the repetitive DNA found in transcribed regions of a non-model organism.
Collapse
Affiliation(s)
- Felipe Cordeiro Dias
- Laboratório de Citogenética e Entomologia Molecular, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Larissa Forim Pezenti
- Laboratório de Citogenética e Entomologia Molecular, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Bioinformática, Universidade Estadual de Londrina, Londrina, Brazil
| | | | | | | | | | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Universidade Estadual de Londrina, Londrina, Brazil
| |
Collapse
|
5
|
Pezenti LF, Levy SM, de Souza RF, Sosa-Gómez DR, da Rosa R. Testes morphology and the identification of transcripts of the hormonal pathways of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Arthropod Struct Dev 2021; 65:101111. [PMID: 34571334 DOI: 10.1016/j.asd.2021.101111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Anticarsia gemmatalis is one of the main defoliating pests of soybeans in Brazil. In the current study, we characterized the histomorphology of the testes and the spermatogenesis process in A. gemmatalis. We also identified transcripts involved in the biosynthesis, metabolism, and signaling of juvenile and ecdysteroid hormones, in order to provide information about potential mechanisms of regulation of hormonal pathways in this species. Our analyses revealed that the A. gemmatalis larvae have a pair of kidney-shaped testicles. These are divided into four testicular follicles, where there are germ cell cysts at different stages of development. In the pupal stage, the testicles are fused, so adults have a single spherical testis, with a variable number of follicles. The A. gemmatalis has centripetal spermatogenesis and exhibits spermatic dimorphism. We identified 31 transcripts that encode proteins involved in juvenile hormone and ecdysteroid pathways, such as mevalonate kinase, CYP14A1, ecdysone receptor, among others. Our results on the morphology of the testes and spermatogenesis process, as well as identification of the genes involved in hormonal pathways in A. gemmatalis, provide important data for understanding the biology of this agricultural pest, which can be used as a basis for further research in other economically important lepidopterans.
Collapse
Affiliation(s)
- Larissa Forim Pezenti
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil; Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Sheila Michele Levy
- Laboratório de Insetos, Departamento de Histologia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Londrina, Paraná, Brazil.
| | - Renata da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| |
Collapse
|
6
|
Pezenti LF, Sosa-Gómez DR, de Souza RF, Vilas-Boas LA, Gonçalves KB, da Silva CRM, Vilas-Bôas GT, Baranoski A, Mantovani MS, da Rosa R. Transcriptional profiling analysis of susceptible and resistant strains of Anticarsia gemmatalis and their response to Bacillus thuringiensis. Genomics 2021; 113:2264-2275. [PMID: 34022342 DOI: 10.1016/j.ygeno.2021.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 03/09/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
Anticarsia gemmatalis is one of the main defoliators of soybean in Brazil. Bacillus thuringiensis (Bt) transgenic crops are used for their management. In this paper we used RNA-seq to explore the response of A. gemmatalis to Bt HD73, as well as to detect transcriptional differences after Bt infection between resistant and susceptible strains. A total of 3853 and 6224 differentially expressed genes (DGEs) were identified in susceptible and resistant larvae after Bt exposure, respectively. We identified 2143 DEGs between susceptible and resistant larvae and 1991 between susceptible and resistant larvae Bt exposed. Immunity-related genes, Bt toxins receptors, proteases, genes involved in metabolic processes, transporters, cuticle proteins and mobile elements have been identified. qRT-PCR data demonstrated upregulation of five genes in susceptible strain after Bt exposure. These results provide insights to understand the molecular and cellular mechanisms of response to Bt that could be used in strategies to control agricultural pests.
Collapse
Affiliation(s)
- Larissa Forim Pezenti
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil; Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Londrina, Paraná, Brazil.
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Laurival Antônio Vilas-Boas
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil; Laboratório de Genética e Taxonomia de Bactérias, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Kátia Brumatti Gonçalves
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | | | - Gislayne Trindade Vilas-Bôas
- Laboratório de Genética e Taxonomia de Bactérias, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Adrivanio Baranoski
- Laboratório de Genética Toxicológica, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Mário Sérgio Mantovani
- Laboratório de Genética Toxicológica, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Renata da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| |
Collapse
|
7
|
Wolf IR, Paschoal AR, Quiroga C, Domingues DS, de Souza RF, Pretto-Giordano LG, Vilas-Boas LA. Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes. BMC Genomics 2018; 19:556. [PMID: 30055586 PMCID: PMC6064168 DOI: 10.1186/s12864-018-4951-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/22/2018] [Indexed: 01/08/2023] Open
Abstract
Background Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae. Results Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types. Conclusions The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-018-4951-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ivan Rodrigo Wolf
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Alexandre Rossi Paschoal
- Universidade Tecnológica Federal do Paraná, Campus Cornélio Procópio, Cornélio Procópio, Paraná, Brazil.
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Douglas Silva Domingues
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, São Paulo, Brazil
| | - Rogério Fernandes de Souza
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | | | - Laurival Antonio Vilas-Boas
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| |
Collapse
|
8
|
Michelan VS, Trevisan R, Silva CRMD, Souza RFD, Luceño M, Vanzela ALL. Morphological and genomic characterization of Rhynchospora tenuis complex (Cyperaceae) and its taxonomic implications. Rodriguésia 2012. [DOI: 10.1590/s2175-78602012000400003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Species of Rhynchospora sect. Tenues are morphologically very similar. Rhynchospora tenuis complex is the most problematic species complex in this group and it concentrates entities of difficult delimitation, as is the case of R. tenuis, R. tenuis subsp. austro-brasiliensis and R. enmanuelis. Samples of these three taxonomic entities, besides R. junciformis and R. breviuscula (Dichromena), were analyzed in a comparative way using morphologic, cytogenetic and molecular tools. Despite of high morphological similarity between these taxa, R. tenuis was separated from R. tenuis subsp. austro-brasiliensis and R. enmanuelis according to chromosome numbers (2n = 4 and 2n = 18) and ISSR markers. The combined analysis of shape and size of achenes and stylopodium, number of spikelets, cytogenetic features and molecular markers suggest a clear proximity among Rhynchospora junciformis, R. tenuis subsp. austro-brasiliensis and R. enmanuelis, in relation to R. tenuis. These data indicate the need for a new taxonomic review of R. sect. Tenues, mainly to solve the status and nomenclatural situation of R. tenuis subsp. austro-brasiliensis and R. enmanuelis.
Collapse
|