Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families

Hernandez-Hernandez, Eric M.; Fernández-Medina, Rita D; Navarro-Escalante, Lucio; Núñez, Jonathan; Machado, Pablo Benavides; Carareto, Claudia M. A.

doi:10.1007/s00438-017-1291-7

Cited by 15 publications

(7 citation statements)

References 71 publications

(72 reference statements)

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“…Hernandez-Hernandez et al . 39 characterized the TEs present in the CBB genome, revealing that 11.51% of the TEs belong to the Tc1/mariner superfamily. Furthermore, the authors confirmed that at least 8.2% of the CBB genome is composed of TEs.…”

Section: Discussionmentioning

confidence: 99%

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Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei

Noriega

Arias

Barbosa

et al. 2019

Sci Rep

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Coffee production is a global industry valued at approximately 173 billion US dollars. One of the main challenges facing coffee production is the management of the coffee berry borer (CBB), Hypothenemus hampei , which is considered the primary arthropod pest of coffee worldwide. Current control strategies are inefficient for CBB management. Although biotechnological alternatives, including RNA interference (RNAi), have been proposed in recent years to control insect pests, characterizing the genetics of the target pest is essential for the successful application of these emerging technologies. In this study, we employed RNA-seq to obtain the transcriptome of three developmental stages of the CBB (larva, female and male) to increase our understanding of the CBB life cycle in relation to molecular features. The CBB transcriptome was sequenced using Illumina Hiseq and assembled de novo . Differential gene expression analysis was performed across the developmental stages. The final assembly produced 29,434 unigenes, of which 4,664 transcripts were differentially expressed. Genes linked to crucial physiological functions, such as digestion and detoxification, were determined to be tightly regulated between the reproductive and nonreproductive stages of CBB. The data obtained in this study help to elucidate the critical roles that several genes play as regulatory elements in CBB development.

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Section: Discussionmentioning

confidence: 99%

“…As discussed by Hernandez-Hernandez et al . 39 , insect reproductive characteristics may be related to low TE content. Haplodiploidy, in which a chromosome set from males is not transmitted to the next generation, prevents the spread of certain TE genes.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei

Noriega

Arias

Barbosa

et al. 2019

Sci Rep

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“…Within the largest insect order, Coleoptera, very little is known regarding TE distribution and evolution. T. castaneum harbors only 6% of TEs (Tribolium Genome Sequencing Consortium et al 2008), Hypothenemus hampei contains 8.2% of TEs (Vega et al 2015; Hernandez-Hernandez et al 2017), while Dichotomius schiffleri harbors 21% (Ic et al 2020). The species closest to S. oryzae , Rhynchophorus ferrugineus, has a TE content of 45% (Hazzouri et al 2020).…”

Section: Resultsmentioning

confidence: 99%

“…The S. oryzae genome is among the most TE-rich insect genomes to date little is known regarding TE distribution and evolution. T. castaneum harbors only 6% of TEs [53], Hypothenemus hampei contains 8.2% of TEs [6,95], while Dichotomius schiffleri harbors 21% [96]. The species closest to S. oryzae, Rhynchophorus ferrugineus, has a TE content of 45% [8].…”

Section: Odorant Receptorsmentioning

confidence: 99%

The transposable element-rich genome of the cereal pestSitophilus oryzae

Parisot

Vargas-Chávez

Goubert

et al. 2021

Preprint

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Background Among beetles, the rice weevil Sitophilus oryzae is one of the most important pests causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce a 770 Mbp assembly, the best for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect symbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. Conclusions In addition to being an agricultural pest and a valuable endosymbiotic system, S. oryzae can be a remarkable model for studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

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“…TE excision can lead to DNA deletions [41], and TE insertion can result in adding DNA through 3 0 and, less frequently, through 5 0 transduction [42,43]. Finally, ectopic recombination between TEs causes [12], >66% [13]) Mus musculus [143], Saccharomyces cerevisiae [144], Arabidopsis thaliana [145], Pyrococcus furiosus [146], Clostridium difficile [147], Danio rerio [133], Kryptolebias marmoratus [148], Bombyx mori [149], Hypothenemus hampei [150], Drosophila melanogaster (11%, [68],~20% [69]), Pseudozyma antarctica, and Laccaria bicolor [151]. Zea mays [152] and Fritillaria imperialis [8].…”

Section: Transposable Elements Are Abundant and Active Genome Denizensmentioning

confidence: 99%

New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Guio

González

2019

Methods in Molecular Biology

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Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.

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Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families

Cited by 15 publications

References 71 publications

Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei

Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei

The transposable element-rich genome of the cereal pestSitophilus oryzae

New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

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