The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori

Dai, Zongrui; Ren, Jianyu; Tong, Xiaoling; Hu, Hai; Lu, Kunpeng; Dai, Fangyin; Han, Minjin

doi:10.3389/fgene.2021.704162

Cited by 6 publications

(4 citation statements)

References 60 publications

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“…In the past years, long-read sequencing has become an attractive alternative to study TE biology. Such reads are able to refine TE annotation (Jiang et al, 2019; Panda & Slotkin, 2020), pinpoint new TE insertions (Mohamed et al, 2020; Rech et al, 2022), determine TE DNA methylation rates at the copy level (Ewing et al, 2020), estimate TE expression (Berrens et al, 2022), and finally, detect TE-gene fusion transcripts (Panda & Slotkin, 2020; Dai et al, 2021; Babarinde et al, 2021). Furthermore, long-read RNA sequencing can not only determine which TE copies are expressed but also discriminate between isoforms of a single TE copy produced by alternative splicing.…”

Section: Introductionmentioning

confidence: 99%

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Rebollo

Cumunel

Mary

et al. 2023

Preprint

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Transposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs are also able to disrupt nearby genes by donating their intrinsic regulatory sequences, as for instance, promoting the ectopic expression of a cellular gene. TE transcription is therefore not only necessary for TE transpositionper sebut can also be associated with TE-gene fusion transcripts, and in some cases, be the product of pervasive transcription. Hence, correctly determining the transcription state of a TE copy is essential to apprehend the impact of the TE in the host genome. Methods to identify and quantify TE transcription have mostly relied on short RNAseq reads to estimate TE expression at the family level, while using specific algorithms to try to discriminate copy-specific transcription. However, assigning short reads to their correct genomic location, and genomic feature is not trivial. Here we retrieved full-length cDNA (TeloPrime, Lexogen) ofDrosophila melanogastergonads and sequenced them using Oxford Nanopore Technologies. We show that long-read RNAseq can be used to identify and quantify TEs at the copy level. In particular, TE insertions overlapping annotated genes are better estimated using long-reads than short-reads. Nevertheless, long TE transcripts (> 5kb) are not well captured. Most expressed TE insertions correspond to copies that have lost their ability to transpose. Some TEs exhibit interesting patterns, such as intronic POGO sequences, which are expressed in ovaries and not testes, in opposition to the host gene. In many instances, we see that TEs can be spliced, independent of their structure or class. Overall, this first comparison of TEs between testis and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.

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Section: Introductionmentioning

confidence: 99%

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Rebollo

Cumunel

Mary

et al. 2023

Preprint

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“…We then combined three approaches including ab initio, homology-based, and transcriptome-based predictions to identify protein-coding genes and their arrangements in the female genome of B. mori . For the ab initio prediction, we used augustus v3.3 ( 62 ) with default parameters to predict genes based on the training set obtained from previous full-length transcriptome ( 63 ). For the homology-based prediction, we used GeMoMa v1.7.1 ( 64 ) with default parameters to perform homology-based prediction based on protein sequence of male B. mori , D. melanogaster , Apis mellifera , and Danaus plexippus .…”

Section: Methodsmentioning

confidence: 99%

Multiple independent origins of the female W chromosome in moths and butterflies

Han,

Luo,

et al. 2024

Sci. Adv.

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Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect ( Bombyx mori ) and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of B. mori . Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.

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“…The mRNA full-length sequence of BmChiNAG was obtained from B. mori full-length transcripts [ 60 ]. The open reading frame (ORF) of BmChiNAG was predicted using the ORF Finder ( , accessed on 27 June 2021).…”

Section: Methodsmentioning

confidence: 99%

The Role of Chitooligosaccharidolytic β-N-Acetylglucosamindase in the Molting and Wing Development of the Silkworm Bombyx mori

Zhang

Luan

et al. 2022

IJMS

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The insect glycoside hydrolase family 20 β-N-acetylhexosaminidases (HEXs) are key enzymes involved in chitin degradation. In this study, nine HEX genes in Bombyx mori were identified by genome-wide analysis. Bioinformatic analysis based on the transcriptome database indicated that each gene had a distinct expression pattern. qRT-PCR was performed to detect the expression pattern of the chitooligosaccharidolytic β-N-acetylglucosaminidase (BmChiNAG). BmChiNAG was highly expressed in chitin-rich tissues, such as the epidermis. In the wing disc and epidermis, BmChiNAG has the highest expression level during the wandering stage. CRISPR/Cas9-mediated BmChiNAG deletion was used to study the function. In the BmChiNAG-knockout line, 39.2% of female heterozygotes had small and curly wings. The ultrastructure of a cross-section showed that the lack of BmChiNAG affected the stratification of the wing membrane and the formation of the correct wing vein structure. The molting process of the homozygotes was severely hindered during the larva to pupa transition. Epidermal sections showed that the endocuticle of the pupa was not degraded in the mutant. These results indicate that BmChiNAG is involved in chitin catabolism and plays an important role in the molting and wing development of the silkworm, which highlights the potential of BmChiNAG as a pest control target.

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The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori

Cited by 6 publications

References 60 publications

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Identification and quantification of transposable element transcripts using Long-Read RNA-seq inDrosophilagermline tissues

Multiple independent origins of the female W chromosome in moths and butterflies

The Role of Chitooligosaccharidolytic β-N-Acetylglucosamindase in the Molting and Wing Development of the Silkworm Bombyx mori

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