Catalogue of bacterial and archaeal Metagenome Assembled Genomes from 'Ledro Alps and Judicaria' UNESCO MAB Biosphere Reserve (North Eastern Italian Alps)

A catalogue of Metagenome Assembled Genomes (MAGs) retrieved from 19 locations within the ‘Ledro Alps and Judicaria’ MAB UNESCO Biosphere Reserve, which comprises a great variety of Alpine freshwater habitats and contributes to a rich and varied biodiversity (https://www.unesco.org/en/mab/ledro-alps-and-judicaria). 19 paired water and surface sediment samples (n=38) were collected along a physiographic gradient including deep and shallow lakes, lake ponds, pasture ponds, ponds and peat bogs. A total of 566 quality-filtered MAGs were initially recovered from the sampled sites. After de-replication, we obtained 496 representative bacterial and archaeal MAGs, with a majority of bacterial MAGs (n=485) and a minority of archaeal MAGs (n=11). We found that 72% (n=352) of the identified bacterial species and 73% (n=8) of the archaeal species were novel, i.e. currently absent in the curated environmental bacterial database GTDB (RS220). In other words, out of 496 MAGs, only 133 bacterial and 3 archaeal MAGs could be classified at the species level based on 95% whole-genome average nucleotide identity (ANI). Regarding completeness and contamination, 36% of bacterial MAGs scored a high-quality score (Completeness > 90% and  Contamination < 5%), while 64% scored a medium-quality score (Completeness > 50% and  Contamination < 10%). 2% of archaeal MAGs had a high-quality and 98% a medium-quality score.

The data presented here include 485 bacterial MAGs (bacteria_metagenome_assembled_genomes.zip) and 11 archaeal MAGs (archaea_metagenome_assemled_genomes.zip), their taxonomic classification data along with genome quality data (bacteria_mag_taxonomy.csv, archaea_mag_taxonomy.csv) and metadata associated to each sample (metadata_samples.csv). The phylogenetic trees (newick files) constructed with the bacterial and archaeal MAGs are also downloadable.

本数据集为采自‘莱德罗阿尔卑斯与朱迪卡里亚’联合国教科文组织人与生物圈（MAB）保护区内19个采样点的宏基因组组装基因组（Metagenome Assembled Genomes，MAGs）目录。该保护区拥有丰富多样的阿尔卑斯淡水生境，孕育了极为丰富的生物多样性（相关介绍链接：https://www.unesco.org/en/mab/ledro-alps-and-judicaria）。
研究团队沿地理环境梯度采集了19组水与表层沉积物配对样本，共计38份，采样生境涵盖深浅湖泊、湖塘、牧场塘、普通池塘及泥炭沼泽。最初从各采样点共获取566条经过质量过滤的MAGs。经去冗余处理后，最终得到496条代表性细菌与古菌MAGs，其中绝大多数为细菌MAGs（共485条），古菌MAGs仅占少数（共11条）。
经分析发现，所鉴定的细菌物种中有72%（共352种）、古菌物种中有73%（共8种）为新发现物种，即目前在经过人工整理的环境细菌数据库基因组分类数据库（Genome Taxonomy Database，GTDB，RS220版本）中无对应记录。换言之，在496条MAGs中，仅有133条细菌MAGs与3条古菌MAGs可基于95%全基因组平均核苷酸一致性（Average Nucleotide Identity，ANI）标准完成物种水平分类。
在基因组完整性与污染率方面，36%的细菌MAGs达到高质量标准（完整性>90%且污染率<5%），剩余64%达到中等质量标准（完整性>50%且污染率<10%）；古菌MAGs中仅2%达到高质量标准，其余98%均为中等质量。
本数据集包含485条细菌MAGs（文件名为bacteria_metagenome_assembled_genomes.zip）与11条古菌MAGs（文件名为archaea_metagenome_assemled_genomes.zip），配套提供这些MAGs的分类学注释数据与基因组质量评估数据（对应文件为bacteria_mag_taxonomy.csv、archaea_mag_taxonomy.csv），以及各采样点的关联元数据（metadata_samples.csv）。基于细菌与古菌MAGs构建的系统发育树（newick格式文件）同样可供下载。