Analysis of transcripts and splice isoforms in red claw crayfish (Cherax quadricarinatus) using single-molecule long-read sequencing

Aquaculture ◽  
2021 ◽  
Vol 541 ◽  
pp. 736828
Author(s):  
Youhou Xu ◽  
Hongping Pan ◽  
Min Lu ◽  
Qingyou Liu ◽  
Laiba Shafique ◽  
...  
Keyword(s):  
Single Molecule ◽  
Splice Isoforms ◽  
Cherax Quadricarinatus ◽  
Long Read ◽  
Red Claw Crayfish

scholarly journals Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Yuehui Chao ◽  
Jianbo Yuan ◽  
Sifeng Li ◽  
Siqiao Jia ◽  
Liebao Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Trifolium Pratense ◽  
Red Clover ◽  
Splice Isoforms ◽  
Long Read ◽  
Trifolium Pratense L

scholarly journals Analysis of Transcripts and splice isoforms in Red Clover (Trifolium pratense L.) by single-molecule long-read sequencing

2018 ◽  
Author(s):  
Yuehui Chao ◽  
Jianbo Yuan ◽  
Sifeng Li ◽  
Siqiao Jia ◽  
Liebao Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Trifolium Pratense ◽  
Intron Retention ◽  
Draft Genome ◽  
Red Clover ◽  
Full Length ◽  
Splice Isoforms ◽  
Single Molecule Level ◽  
Long Read ◽  
Novel Isoforms

AbstractRed clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover. In this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2,194 novel isoforms from novel genes were identified. A total of 5,492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8,719 including 1,86,517 transcripts have at least one poly(A) site. Furthermore, we identified 4,333 long non-coding RNAs and 3,762 fusion transcripts. Our results show the feasibility of deep sequencing full-length RNA from red clover transcriptome on a single-molecule level.

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

2020 ◽  
Vol 295 (2) ◽  
pp. 475-489 ◽  
Author(s):  
Lijuan Xie ◽  
Ke Teng ◽  
Penghui Tan ◽  
Yuehui Chao ◽  
Yinruizhi Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Perennial Ryegrass ◽  
Splice Isoforms ◽  
Long Read

scholarly journals The dynamic landscape of fission yeast meiosis alternative-splice isoforms

2016 ◽  
Author(s):  
Zheng Kuang ◽  
Jef D. Boeke ◽  
Stefan Canzar
Keyword(s):  
Alternative Splicing ◽  
Fission Yeast ◽  
Single Molecule ◽  
Intron Retention ◽  
Major Type ◽  
Splice Isoforms ◽  
Long Read ◽  
Dynamic Landscape ◽  
Yeast Meiosis ◽  
Novel Isoforms

AbstractAlternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter, to characterize the transcriptome in the meiosis of fission yeast. We reveal 17017 alternative splicing events in 19741 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by “alternate intron in exon”. 887 novel transcription units are detected; 60 of the predicted proteins show homology in other species and form theoretical stable structures. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but the possibility of functional novel isoforms is not excluded. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, this study highlights the diversity and dynamics at the isoform level in the sexual development of fission yeast.

scholarly journals Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

BMC Cancer ◽  
2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Lucia Cavelier ◽  
Adam Ameur ◽  
Susana Häggqvist ◽  
Ida Höijer ◽  
Nicola Cahill ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Splice Isoforms ◽  
Long Read ◽  
Clonal Distribution

scholarly journals Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balázs Kakuk ◽  
Dóra Tombácz ◽  
Zsolt Balázs ◽  
Norbert Moldován ◽  
Zsolt Csabai ◽  
...  
Keyword(s):  
Single Molecule ◽  
Splice Variants ◽  
Splice Isoforms ◽  
Short Read Sequencing ◽  
Novel Transcript ◽  
Novel Approach ◽  
Oxford Nanopore ◽  
Long Read ◽  
Polycistronic Transcripts ◽  
Oxford Nanopore Technologies

AbstractLong-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.

scholarly journals Combined Nanopore and Single-Molecule Real-Time Sequencing Survey of Human Betaherpesvirus 5 Transcriptome

2021 ◽  
Author(s):  
Balazs Kakuk ◽  
Dora Tombacz ◽  
Zsolt Balazs ◽  
Norbert Moldovan ◽  
Zsolt Csabai ◽  
...  
Keyword(s):  
Single Molecule ◽  
Splice Variants ◽  
Splice Isoforms ◽  
Short Read Sequencing ◽  
Novel Transcript ◽  
Novel Approach ◽  
Oxford Nanopore ◽  
Long Read ◽  
Polycistronic Transcripts ◽  
Oxford Nanopore Technologies

Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.

Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing

2019 ◽  
Vol 99 (3) ◽  
pp. 219-235 ◽  
Author(s):  
Yuehui Chao ◽  
Jianbo Yuan ◽  
Tao Guo ◽  
Lixin Xu ◽  
Zhiyuan Mu ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Single Molecule ◽  
Splice Isoforms ◽  
Long Read ◽  
Medicago Sativa L

scholarly journals Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayako Nishizawa ◽  
Kazuki Kumada ◽  
Keiko Tateno ◽  
Maiko Wagata ◽  
Sakae Saito ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Polymorphisms ◽  
Genomic Dna ◽  
Genomic Sequences ◽  
Genomic Sequencing ◽  
Public Database ◽  
Coding Sequences ◽  
Pacbio Rs Ii ◽  
Potential Association ◽  
Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

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