德国欧洲分子生物学实验室Peer Bork等研究人员合作绘制出原核基因的生物地理学图谱。相关论文于2021年12月15日在线发表在《自然》杂志上。

研究人员从14个主要栖息地的13174个公开的元基因组中构建了一个非冗余的基因目录，包括3.03亿个物种级别的基因（以95%的核苷酸身份聚类），并利用它来表明大多数基因是特定于单一栖息地的。在多个栖息地发现的一小部分基因富集在抗生素抗性基因和移动遗传元素的标记中。通过进一步将这些物种级基因聚类到3200万个蛋白家族中，研究人员观察到这些家族中的一小部分包含了大部分的基因（0.6%的家族占50%的基因）。大多数物种水平的基因和蛋白质家族是罕见的。此外，物种级基因，特别是罕见的基因，显示出较低的正向（适应性）选择率，从而支持了一种模型，即在每个蛋白质家族中观察到的大多数遗传变异性是中性或接近中性的。

据介绍，微生物基因编码了地球上生命的大部分功能图谱。然而，尽管在各种栖息地的元基因组测序方面做出了越来越多的努力，但对全球生物圈的基因分布却知之甚少，这对人类和地球的健康有影响。

附：英文原文

Title: Towards the biogeography of prokaryotic genes

Author: Coelho, Luis Pedro, Alves, Renato, del Ro, lvaro Rodrguez, Myers, Pernille Neve, Cantalapiedra, Carlos P., Giner-Lamia, Joaqun, Schmidt, Thomas Sebastian, Mende, Daniel R., Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofia K., Khedkar, Supriya, Maistrenko, Oleksandr M., Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Zhao, Xing-Ming, Nielsen, Henrik Bjrn, Huerta-Cepas, Jaime, Bork, Peer

Issue&Volume: 2021-12-15

Abstract: Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1,2,3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.

DOI: 10.1038/s41586-021-04233-4

Source: https://www.nature.com/articles/s41586-021-04233-4