Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing

L Zhao, H Zhang, MV Kohnen, KVSK Prasad… - Frontiers in …, 2019 - frontiersin.org
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences
(PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are …

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

M Wang, L Tu, D Yuan, D Zhu, C Shen, J Li, F Liu… - Nature …, 2019 - nature.com
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long
been cultivated worldwide for natural renewable textile fibers. The draft genome sequences …

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

I Jabre, ASN Reddy, M Kalyna… - Nucleic Acids …, 2019 - academic.oup.com
Plants display exquisite control over gene expression to elicit appropriate responses under
normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that …

Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

M Sun, D Huang, A Zhang, I Khan, H Yan, X Wang… - BMC Plant …, 2020 - Springer
Background Heat and drought are serious threats for crop growth and development. As the
sixth largest cereal crop in the world, pearl millet can not only be used for food and forage …

The developmental dynamics of the Populus stem transcriptome

Q Chao, ZF Gao, D Zhang, BG Zhao… - Plant biotechnology …, 2019 - Wiley Online Library
The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary
growth (radial growth), which produces biomass that is an important source of energy …

PacBio fulllength cDNA sequencing integrated with RNAseq reads drastically improves the discovery of splicing transcripts in rice

G Zhang, M Sun, J Wang, M Lei, C Li, D Zhao… - The Plant …, 2019 - Wiley Online Library
In eukaryotes, alternative splicing (AS) greatly expands the diversity of transcripts. However,
it is challenging to accurately determine fulllength splicing isoforms. Recently, more studies …

A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis

J Ye, S Cheng, X Zhou, Z Chen, SU Kim, J Tan… - Industrial Crops and …, 2019 - Elsevier
Ginkgo biloba, which contains flavonoids as bioactive components, is widely used in
traditional Chinese medicine. Increasing the flavonoid production of medicinal plants …

Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation

MX Chen, FY Zhu, B Gao, KL Ma, Y Zhang… - Plant …, 2020 - academic.oup.com
Rice (Oryza sativa) molecular breeding has gained considerable attention in recent years,
but inaccurate genome annotation hampers its progress and functional studies of the rice …

The catalase gene family in cotton: genome-wide characterization and bioinformatics analysis

W Wang, Y Cheng, D Chen, D Liu, M Hu, J Dong… - Cells, 2019 - mdpi.com
Catalases (CATs), which were coded by the catalase gene family, were a type notably
distinguished ROS-metabolizing proteins implicated to perform various physiological …

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe

S Feng, M Xu, F Liu, C Cui, B Zhou - BMC plant biology, 2019 - Springer
Abstract Background Gossypium australe F. Mueller (2 n= 2 x= 26, G 2 genome) possesses
valuable characteristics. For example, the delayed gland morphogenesis trait causes …