Tran, H.-D. | Search bioRxiv

bioRxiv2026

Integrative identification of Tetratostichococcus sp. CCAH0201 (Trebouxiophyceae, Chlorophyta) from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam

A microalgal strain from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam, was examined by light microscopy and three molecular markers. Thirty-six cells from 22 micrographs measured 6.68-12.74 by 3.49-4.79 micrometres. Homologous phylogenetic windows comprised 550 nucleotides for SSU rDNA, 711 for ITS and 1,170 for rbcL. CCAH0201, P1 and Tetratostichococcus jenerensis SAG 2138 shared the SSU 3-prime sequence, whereas ITS and rbcL placed CCAH0201 with P1 (SH-aLRT/UFBoot 87/94 and 96.9/99). CCAH0201 differed from P1 at 22/711 ITS and 4/1,170 rbcL sites. Structure-guided ITS2 comparison identified one strict CBC, one two-sided change from a wobble pair and three hemi-CBCs relative to P1. CCAH0201 is thus identified as Tetratostichococcus sp. in a lineage close to P1.

microbiology↗

bioRxiv2021

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

genomics↗