A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.

ABSTRACT: Short-read metabarcoding analysis is the gold standard for accessing partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible, but with low read accuracy. Moreover, 16S rRNA gene amplification in seaweed results in a large proportion of plastid reads, which are directly or indirectly derived from cyanobacteria. Primers designed not to amplify plastid sequences are available for short-read sequencing, while Oxford Nanopore Technology (ONT) offers adaptive sampling, a unique way to remove reads in real time. In this study, we compare three options to address the issue of plastid reads: deleting plastid reads with adaptive sampling, using optimised primers with Illumina MiSeq technology, and sequencing

SUBMITTER: Rousseau C 

PROVIDER: S-EPMC12415815 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature