Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-seq

Xu, Danping; Yang, Hui; Zhuo, Zhihang; Lu, Binfeng; Hu, Jingjing; Yang, Fan

doi:10.1016/j.ijbiomac.2020.12.098

Cited by 9 publications

(15 citation statements)

References 76 publications

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“…Although the high-quality reference genome has been released in 2019 ( Kawamoto et al, 2019 ), the transcriptome so far was obtained through assembling short reads resulting in poor-quality transcripts and incorrect genome annotation ( Shao et al, 2012 ; Suetsugu et al, 2013 ). Recently, with the development of sequencing technology, PacBio sequencing, which has a profound advantage in long reads, has been applied widely to generate high-quality full-length transcripts in eukaryotes ( Sharon et al, 2013 ; Wang et al, 2016 ; Jiang et al, 2019 ; Wang et al, 2019 ; Yang et al, 2020 ; Xu et al, 2021 ). In this study, we identified 25,970 high-quality transcripts in the silkworm by using PacBio sequencing technology.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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The domesticated silkworm, Bombyx mori, is an important model system for the order Lepidoptera. Currently, based on third-generation sequencing, the chromosome-level genome of Bombyx mori has been released. However, its transcripts were mainly assembled by using short reads of second-generation sequencing and expressed sequence tags which cannot explain the transcript profile accurately. Here, we used PacBio Iso-Seq technology to investigate the transcripts from 45 developmental stages of Bombyx mori. We obtained 25,970 non-redundant high-quality consensus isoforms capturing ∼60% of previous reported RNAs, 15,431 (∼47%) novel transcripts, and identified 7,253 long non-coding RNA (lncRNA) with a large proportion of novel lncRNA (∼56%). In addition, we found that transposable elements (TEs) exonization account for 11,671 (∼45%) transcripts including 5,980 protein-coding transcripts (∼32%) and 5,691 lncRNAs (∼79%). Overall, our results expand the silkworm transcripts and have general implications to understand the interaction between TEs and their host genes. These transcripts resource will promote functional studies of genes and lncRNAs as well as TEs in the silkworm.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…The RNA was transformed into cDNA using the Hiscript III Reverse Transcription Kit (Vazyme, Nanjing, China), and fluorescent quantitative PCR was performed on an ABI 7500 (Thermo, MA, United Sttaes) using the AceQ qPCR SYBR Green Master Mix system (Vazyme, Nanjing, China). The relative quantitative 2 −ΔΔCt method was used to analyze genes expression ( Xu et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Sequencing Analysis of Hirudo nipponia in Different Growth Periods

Yan

et al. 2022

Front. Physiol.

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Hirudo nipponia is the only blood-sucking leech included in Chinese Pharmacopoeia having distinct features of anticoagulation, exorcizing blood stasis, and promoting menstruation. Despite such significant characteristics, very little is known about its molecular genetics and related physiological mechanisms. In this study, the transcriptomes of H. nipponia at three developmental stages (larvae, young, and adults), revealed a total of 1,348 differentially expressed genes (DEGs), 223 differentially expressed lncRNAs, and 88 novel mRNAs. A significant diverse gene expression patterns were observed at different developmental stages which were analyzed by differential gene expression trends, and the overall gene expression trends consist of three overall down-regulated trends, and two overall up-regulated trends. Furthermore, the GO and KEGG enrichment functional annotation analysis revealed that these DEGs were mainly associated with protein hydrolysis, signal transduction, energy metabolism, and lipid metabolism while growth, development, metabolism, and reproduction-related DEGs were also found. Additionally, real-time quantitative PCR results confirmed deep sequencing results based on the relative expression levels of nine randomly selected genes. This is the first transcriptome-based comprehensive study of H. irudo nipponia at different developmental stages which provided considerable deep understanding related to gene expression patterns and their relevant developmental pathways, neurodevelopmental and reproductive characteristics of the leech.

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“…Eighteen samples (AhWr1, AhWr2, AhWr3; AhWs1, AhWs2, AhWs3; AhWf1, AhWf2, AhWf3; AhCr1, AhCr2, AhCr3; AhCs1, AhCs2, AhCs3; AhCf1, AhCf2, and AhCf3) were used for RNA extraction, and total RNA from the 18 samples was used for Illumina sequencing. For SMRT sequencing, total RNA from the 18 samples was mixed for subsequent experiments, according to previous studies [49][50][51][52].…”

Section: Plant Materialsmentioning

confidence: 99%

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

Meng

Zhang

et al. 2021

BMC Genomics

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Background Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis. Results We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as ‘photosynthesis’, ‘carbon fixation in photosynthetic organisms’, ‘glycolysis/gluconeogenesis’, and ‘TCA cycle’. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF–DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG–SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth. Conclusions Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.

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Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-seq

Cited by 9 publications

References 76 publications

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

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

Comparative Transcriptome Sequencing Analysis of Hirudo nipponia in Different Growth Periods

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

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