Bandeau MISTIC

Assembly and annotation of genomes from soil metagenomic data

Postdoctoral research project as part of the MISTIC project, supervised by INRAE.

  • Title: "Assembly and annotation of genomes from soil metagenomic data" ; INRAE.
    • Postdoctoral researcher: Carole Belliardo.
    • Affiliated unit: INRAE, UMR 1356 - ISA - GAME.
    • Project duration: 2023–2024.

Project summary:

The soil microbiome remains poorly understood, but it is crucial to uncover its genetic diversity, given the essential functions primarily carried out by its arsenal of proteins. While short-read (SR) metagenomics has provided valuable insights into the gene diversity of the microbiome, it has not yielded complete reconstructions of microbial genomes. Metagenome-assembled genomes (MAGs) obtained through short-read metagenomics often result in fragmented assemblies and incomplete gene sets that are unusable for gene prediction. Using PacBio's high-precision long-read sequencing (HiFi), we previously obtained long reads from tunnel-cultivated soil metagenomes, surpassing the contig length of publicly available short-read metagenomes. Although a substantial portion of the reads remains unassembled, we have successfully reconstructed dozens of metagenome-assembled genomes, further improving the contiguity of reads encompassing bacterial, archaeal, and viral genomes from terrestrial environments. To more comprehensively compare long-read and short-read approaches, we generated ultra-deep short-read sequencing on the same soil sample. Although the contigs are significantly shorter with short-read technology, ultra-deep sequencing appears to have captured a greater diversity of taxa than long-read sequencing. However, this impression needs to be confirmed by an independent metabarcoding method. High-precision long-read sequencing holds significant potential for elucidating the complexity of bacterial genome reconstruction. Nevertheless, several critical considerations remain to be addressed, such as the sequencing depth required to capture and reconstruct a meaningful representation of the true biodiversity in soil microbiomes.

See also