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A genome and gene catalog of glacier microbiomes

Abstract

Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.

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Fig. 1: Geographical distribution of metagenome-assembled genomes.
Fig. 2: TGGs reveal the uniqueness of the microbiome in the glacier ecosystem.
Fig. 3: Functional novelty of the TG2G catalog.
Fig. 4: TGGs harbor a diverse range of potential pathogenic factors.
Fig. 5: Principal component analysis plots of Tibetan, Alps and Arctic glacier microbial communities.

Data availability

The TG2G catalog is organized in three levels: Assembled contigs, Genes and Genomes (Supplementary Fig. 9). The assembled contig section contains the sequence of non-redundant contigs and the coverage of each contig across all samples; the gene section contains the sequences of non-redundant ORFs, the coverage of each gene across all samples and the annotation of all genes using eggNOG, CARD, CAZy, COG, VFDB and KEGG; and the genome section contains the genomes quality assessment file, taxonomic classification, the representative genomes of OTUs and their coverage across all samples, as well as the annotation of genes against the same databases as the gene section of the catalog. The catalog in the structure described is available at the National Omics Data Encyclopedia under project ID OEP003083. Raw reads are also deposited in the NCBI under the project Tibetan Glacier Genome and Gene Catalogue (PRJNA813429) with SRA numbers SRR18576994–SRR18577078 (ref. 69). Additional global glacier metagenomes were downloaded from the NCBI under project IDs PRJNA445613, PRJNA360211, PRJEB12327 and PRJNA283341. The supplementary table file is available at https://doi.org/10.6084/m9.figshare.19766653.

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Acknowledgements

This study was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (STEP) 2019QZKK0503 (Y. Liu and K.L.) and 2021QZKK0100 (P.L., Y. Luo and T. Yu); the National Key Research and Development Plans 2019YFC1509103 (Y. Liu) and 2021YFC2300904 (M.J.); and the Major Research Plan of the National Natural Science Foundation of China 91851207 (Y. Liu and Y.C.).

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Y. Liu, M.J. and T. Yao designed the study. T. Yu, Z.Z., Y. Luo and Y.C. performed the analyses. Y. Liu and M.J. led the writing of the manuscript, with results interpretations from J.Z., A.M.A., P.H., S.H., P.L. and K.L. All authors contributed to the editing of the text and approved the final version.

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Correspondence to Yongqin Liu or Yingfeng Luo.

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Nature Biotechnology thanks Stefanie Lutz and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Liu, Y., Ji, M., Yu, T. et al. A genome and gene catalog of glacier microbiomes. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01367-2

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