Direct RNA Sequencing Unfolds the Complex Transcriptome of Vibrio parahaemolyticus

Abstract

Vibrio parahaemolyticus is a halophilic bacterium found in the marine environment. Outbreaks of gastroenteritis resulting from seafood poisoning by these pathogens have risen over the past 2 decades.

The use of RNA-seq for the study of physiological adaptations of halophiles in extreme environments for astrobiological data interpretation

“…Z-M001 (Yang et al, 2020), Jeotgalibacillus malaysiensis (Yaakop et al, 2016), Natrinema sp. J7-2 (Mei et al, 2017), Tetragenococcus halophilus (Liu et al, 2015;Yao et al, 2022), Vibrio parahaemolyticus (Al Kadi et al, 2021;Li et al, 2022;Zhang et al, 2023). Besides these, metagenomic analysis using RNA-seq was performed to study the genetic diversity of multiple halophilic microorganisms (Cycil et al, 2020).…”

Microbial Single-Cell Analysis: What Can We Learn From Mammalian?

“…Furthermore, new techniques developed for bulk cells, such as the CUT&Tag technique for histone modification detection ( Kaya-Okur et al, 2019 ), the EM-seq ( Feng et al, 2020 ; Sun et al, 2021 ; Vaisvila et al, 2021 ) and TAPS ( Liu et al, 2019 ) techniques for DNA methylation detection, and DLO-HiC ( Lin et al, 2018 ), BAT Hi-C ( Huang et al, 2020 ) and tagHi-C ( Zhang et al, 2020 ) techniques for improved Hi-C library preparation, may also be capable for single cells, even with several modifications. Finally, current sequencing techniques have made it possible to directly obtain the DNA, RNA, and protein sequences without amplification, making the direct sequencing of individual cells is worth waiting in the coming future ( Al Kadi et al, 2021 ; Brinkerhoff et al, 2021 ; Mohammadi and Bavi, 2021 ; Pust et al, 2021 ; Pyatnitskiy et al, 2021 ).…”

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing ofEscherichia coliisolates

“…Recent advances in long-read sequencing, for example from Oxford Nanopore Technologies (ONT; hereafter referred to as "nanopore"), have removed the need for RNA fragmentation thus permitting sequencing of longer transcripts, and improved read-mapping strategies and transcript identification [7]. Nanopore RNA-Seq protocols reflect two main approaches: The first is direct sequencing of RNA molecules using the RNA-Seq kit (SQK-RNA002, upgraded to SQK-RNA004 in early 2024 for compatibility with the latest Early Access program RNA (FLO-MIN004RA) flow cell) [7][8][9]. The second incorporates cDNA synthesis allowing enrichment of full-length sequenced transcripts [7].…”

“…To date, most RNA-Seq has been based on short-read Illumina sequencing generating read lengths up to 300bp, and short-read RNA-Seq workflows and computational tools have evolved substantially [2, 5]. During library preparation for short-read sequencing however, RNA is fragmented prior to reverse transcription (RT), potentially resulting in lost information during read mapping and making distinguishing between overlapping transcripts and therefore full-length transcript analysis challenging [7, 8]. Recent advances in long-read sequencing, for example from Oxford Nanopore Technologies (ONT; hereafter referred to as “nanopore”), have removed the need for RNA fragmentation thus permitting sequencing of longer transcripts, and improved read-mapping strategies and transcript identification [7].…”