Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution

• Published in: Molecular genetics and genomics : MGG Vol. 298; no. 6; pp. 1377 - 1388
• Main Authors: Dionisio, Jaqueline Fernanda, Pezenti, Larissa Forim, de Souza, Rogério Fernandes, Sosa-Gómez, Daniel Ricardo, da Rosa, Renata
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.11.2023; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biochemistry; Biomedical and Life Sciences; Brazil; Chromosomes; class; Cytogenetics; DNA; DNA probes; DNA Transposable Elements - genetics; Euschistus heros; Euschistus servus; fluorescence; Fluorescence in situ hybridization; genome; genomics; Horizontal transfer; Human Genetics; hybridization; In Situ Hybridization, Fluorescence; insects; Life Sciences; Long interspersed nucleotide elements; Microbial Genetics and Genomics; Neotropics; Nucleotide sequence; Original Article; Phylogeny; Plant Genetics and Genomics; Retroelements; retrotransposons; sequence analysis; soybeans; species; transcription (genetics); transcriptome; Transcriptome - genetics; Transcriptomes; Transposons; Brazil; Holocentric chromosomes; Repetitive DNA; Fluorescent in situ hybridization; RNA-Seq; Hemiptera
• ISSN: 1617-4615; 1617-4623; 1617-4623
• DOI: 10.1007/s00438-023-02063-9

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.