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

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.

Download Full-text

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

Molecular Genetics and Genomics ◽

10.1007/s00438-019-01635-y ◽

2020 ◽

Vol 295 (2) ◽

pp. 475-489 ◽

Cited By ~ 1

Author(s):

Lijuan Xie ◽

Ke Teng ◽

Penghui Tan ◽

Yuehui Chao ◽

Yinruizhi Li ◽

...

Keyword(s):

Single Molecule ◽

Perennial Ryegrass ◽

Splice Isoforms ◽

Long Read

Download Full-text

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

10.1101/045922 ◽

2016 ◽

Cited By ~ 2

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.

Download Full-text

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

BMC Cancer ◽

10.1186/s12885-015-1046-y ◽

2015 ◽

Vol 15 (1) ◽

Cited By ~ 28

Author(s):

Lucia Cavelier ◽

Adam Ameur ◽

Susana Häggqvist ◽

Ida Höijer ◽

Nicola Cahill ◽

...

Keyword(s):

Rna Sequencing ◽

Single Molecule ◽

Splice Isoforms ◽

Long Read ◽

Clonal Distribution

Download Full-text

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

Scientific Reports ◽

10.1038/s41598-021-93593-y ◽

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.

Download Full-text

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

10.1101/2021.03.30.437686 ◽

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.

Download Full-text

Estimación de biomasa aérea de forrajes de invierno bajo riego a través de un dron

RECUBRIMIENTO COMESTIBLE CON BASE DE PIÑON MEXICANO (Jatropha curcas) SOBRE LA CALIDAD DE CHAYOTE MINIMAMENTE PROCESADO ◽

10.32854/agrop.v0i0.354 ◽

2019 ◽

Vol 12 (4) ◽

Author(s):

Francisco Gavi Reyes ◽

César Botello-Aguillón ◽

Leonardo Tijerina-Chávez ◽

Arturo Galvis-Spíndola ◽

Rodrigo Roblero-Hidalgo

Keyword(s):

Medicago Sativa ◽

Avena Sativa ◽

Medicago Sativa L

E Objetivo: Desarrollar un procedimiento para estimar biomasa con imágenes digitales captadas desde un dron y modelación 3D (ID-Dron-3D) aplicable en alfalfa (Medicago sativa L.) y avena forrajera (Avena sativa L.). Diseño/metodología/aproximación: Con una cámara digital acoplada al dron se obtuvieron imágenes antes de la cosecha de los cultivos, que fueron procesadas con software para luego estimar volumen de biomasa. En cada cultivo se midió altura de la planta y área cosechada, volumen aparente y real de biomasa, y peso de biomasa fresca y seca. Resultados: Con base en el análisis de regresión se obtuvieron modelos lineales a una p<0.05 para predecir: biomasa fresca en avena (R2=0.70) y alfalfa (R2 =0.47); y biomasa seca en avena (R2=0.78) y en alfalfa (R2=0.31) mediante ID-Dron-3D. Limitaciones del estudio/implicaciones: Considerando las R2 de los modelos obtenidos, los resultados en la avena forrajera fueron mejores, respecto a los detectados en alfalfa, lo cual se puede deber a la mayor variabilidad de la cobertura vegetal, ya que, en algunas unidades de muestreo, las plantas de alfalfa no cubrían completamente el suelo. Hallazgos/conclusiones: El rendimiento de biomasa fresca y seca de ambos cultivos se correlacionó significativamente con su respectivo volumen aparente estimado con imágenes digitales tomadas desde un dron y su procesamiento 3D (ID-Dron-3D).

Download Full-text

ALFALFA (Medicago sativa L.) CULTIVADA EN CAMPECHE, MÉXICO Y SU INTEGRACIÓN LOCAL EN LA ALIMENTACIÓN DE CORDEROS EN CONFINAMIENTO

RECUBRIMIENTO COMESTIBLE CON BASE DE PIÑON MEXICANO (Jatropha curcas) SOBRE LA CALIDAD DE CHAYOTE MINIMAMENTE PROCESADO ◽

10.32854/agrop.v11i9.1217 ◽

2018 ◽

Vol 11 (9) ◽

Author(s):

CC. Castillo-Águilar

Keyword(s):

Medicago Sativa ◽

Pennisetum Purpureum ◽

Medicago Sativa L

Se comparó el uso de diferentes dietas con base en heno de alfalfa cultivada (Medicago sativa L.) en Campeche y su relación con un concentrado comercial y pasto Taiwán (Pennisetum purpureum), T1=concentrado comercial, T2=T1+heno de alfalfa, T3=T1+pasto Taiwán, T4=heno de alfalfa. Se evaluó el comportamiento productivo y metabólico de corderos en sistema intensivo utilizando 20 corderos machos con encaste de Pelibuey, Dorper y Black Belly de 12.5±1 kg de peso vivo (PV). Se midió el consumo de materia seca total (CMS), la ganancia diaria de peso (GDP), la conversión alimenticia (CA), y la digestibilidad in situ de la materia seca (DISMS). También fueron evaluados el pH, nitrógeno amoniacal (NH3) y la concentración de ácidos grasos volátiles (AGV) en líquido ruminal. La mejor GDP en gramos por día, de 234 g (p?0.05) se obtuvo en el T2; en contraste, el T3 mostró la menor GDP. La dieta que incluyó la mezcla de heno de alfalfa y concentrado mejoró significativamente las condiciones de las variables pH, NH3 y AGV (p?0.05).

Download Full-text