Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

• Published in: Molecular ecology resources 2023-07, Vol.23 (5), p.1066-1076
• Main Authors: Saraiva, Joao Pedro, Bartholomäus, Alexander, Toscan, Rodolfo Brizola, Baldrian, Petr, Nunes da Rocha, Ulisses
• Format: Article
• Language: English
• Subjects: Anthropogenic factors; Bins; Chromosomes; Completeness; Ecosystem; Eukaryota - genetics; eukaryotes; Fungi - genetics; Gene mapping; Genome, Microbial; Genomes; genome‐resolved metagenomics; Hypocreales; Mamiellales; Metagenome; Metagenomics; Microorganisms; Reconstruction; Recovery; Saccharomycetales
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.13776

As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host‐associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single‐copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long‐read sequencing, development of tools for dealing with repeat‐rich genomes, and improved reference genomes databases.