Reconstruction of small subunit ribosomal RNA from high‐throughput sequencing data: A comparative study of metagenomics and total RNA sequencing
نویسندگان
چکیده
The small subunit (SSU) ribosomal RNA (rRNA) is the most commonly used marker for identification of microbial taxa, but its full-length reconstruction from high-throughput sequencing (HTS) data remains challenging. Metagenomics and total (total RNA-Seq) are target-PCR-free HTS methods that to characterize communities simultaneously reconstruct SSU rRNA sequences. However, more testing required determine improve their effectiveness. We processed metagenomics RNA-Seq retrieved a commercially available mock community an aquarium sample using 112 combinations processing tools. determined completeness both samples analysed impact tools on completeness. In contrast metagenomics, allowed complete or near-complete all sequences generated up 438 with ≥80% only 1/5 Illumina MiSeq run. significantly correlated genome size species. Data impacted completeness, in particular utilized assemblers. These results promising novel could advance simultaneous application multiple -omics approaches routine environmental assessments allow holistic ecosystems.
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ژورنال
عنوان ژورنال: Methods in Ecology and Evolution
سال: 2023
ISSN: ['2041-210X']
DOI: https://doi.org/10.1111/2041-210x.14149