PacBio single-molecule long-read sequencing shed new light on the transcripts and splice isoforms of the perennial ryegrass

Xie, Liji; Teng, Ke; Tan, Penghui; Chao, Yuehui; Li, Yinruizhi; Guo, Weier; Han, Liebao

doi:10.1007/s00438-019-01635-y

Cited by 23 publications

(19 citation statements)

References 43 publications

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“…Furthermore, we analyzed the consensus motif around donor and acceptor sites, polyadenylation sites, and (TSS). We found that the splicing donor and acceptor sites have conserved GT-AG consensus motif ( Figures 2A,B ), which is consistent with the other organism such as perennial ryegrass ( Xie, et al, 2020 ), B. malayi (Nicolas J Wheeler, et al, 2020 ), and Medicago sativa L. ( Chao, et al, 2019 ). In addition, the result of polyadenylation sites analysis indicates that “AAUAAA” has the highest frequency ( Figure 2C ).…”

Section: Resultssupporting

confidence: 85%

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: Resultssupporting

confidence: 85%

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 third-generation sequencing technology signified by Pacific Biosciences (PacBio, Menlo Park, CA, USA) effectively overcome this problem [ 19 , 20 ]. Single-molecule real-time (SMRT) sequencing can directly obtain full-length splice isoforms without the need for assembly [ 21 , 22 ], improve the draft genome annotation in species with reference genome and facilitate comparative transcriptome studies and gene functional annotation [ 22 ]. Up to date, this technology has been successfully utilized in some species, such as perennial ryegrass ( Lolium perenne ) [ 22 ], Rhododendron lapponicum [ 23 ], strawberry ( Fragaria × ananassa ) [ 24 ], Gnetum luofuense [ 25 ], and maize ( Zea mays ) [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

Zaman

et al. 2021

Plants

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This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

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“…PacBio sequencing technique is an efficient approach to sequence long DNA molecules, leading to its widely application in full-length reference transcriptome construction of many plant species ( Teng et al, 2019 ; Zhou et al, 2019 ; Xie et al, 2020 ). However, due to the inherent high error rate, transcriptome analyses based on PacBio sequencing is error prone and requires adjustment ( Mahmoud et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Cynodon dactylon L.)

Chen

et al. 2021

Front. Genet.

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As an important warm-season turfgrass and forage grass species with wide applications, bermudagrass (Cynodon dactylon L.) simultaneously has shoot, stolon and rhizome, three types of stems with different physiological functions. To better understand how the three types of stems differentiate and specialize, we generated an organ-specific transcriptome dataset of bermudagrass encompassing 114,169 unigenes, among which 100,878 and 65,901 could be assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) terms, respectively. Using the dataset, we comprehensively analyzed the gene expression of different organs, especially the shoot, stolon and rhizome. The results indicated that six organs of bermudagrass all contained more than 52,000 significantly expressed unigenes, however, only 3,028 unigenes were enrich-expressed in different organs. Paired comparison analyses further indicated that 11,762 unigenes were differentially expressed in the three types of stems. Gene enrichment analysis revealed that 39 KEGG pathways were enriched with the differentially expressed unigenes (DEGs). Specifically, 401 DEGs were involved in plant hormone signal transduction, whereas 1,978 DEGs were transcription factors involved in gene expression regulation. Furthermore, in agreement with the starch content and starch synthase assay results, DEGs encoding starch synthesis-related enzymes all showed the highest expression level in the rhizome. These results not only provided new insights into the specialization of stems in bermudagrass but also made solid foundation for future gene functional studies in this important grass species and other stoloniferous/rhizomatous plants.

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PacBio single-molecule long-read sequencing shed new light on the transcripts and splice isoforms of the perennial ryegrass

Cited by 23 publications

References 43 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

Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

Organ-Specific Transcriptome Analysis Identifies Candidate Genes Involved in the Stem Specialization of Bermudagrass (Cynodon dactylon L.)

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