Pearl River estuary microbiome and virome

Project description: Deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary (PRE), a typical subtropical. Data description: Data for assembly, MAGs, viral like contigs and populations generated using the PRE microbial metagenomic data sets - data includes:PRET1608S??F00_idba-ud_final.fna.gz: the contigs generated from virome(<0.2 μm) (5 files).PRET1608S??F0{2/7}_megahit_final.fna.gz: the contigs generated from cellular metagenome(0.2-0.7 μm and 0.7-2.7μm) (10 files).PRET1608S??F0{2/7}_MAGs.tar.gz: MAGs with ≥ 50% completeness and ≤ 10% contamination of each metagenome. PRE_all_dereplicated_MAGs.tar.gz: 1,205 non-redundant prokaryotic genomes with ≥ 50% completeness and ≤ 10% contamination. PRE_viral_contigs.fasta: Putative viral contigs identified from contigs of all the three size fractions in PRE (1 file).PRE_viral_contigs_95-80.fna: Viral populations based on 95% nucleotide identity and 80% of the genome coverage criterion (1 file).Table1-SingleCopyMarkers.xlsx: The information of 122 archaeal single-copy marker proteins and 120 bacterial single-copy marker proteins were used to infer the maximum likelihood trees of archaeal and bacterial phylogenetic trees, respectively (1 file). Table2-MAGsGTDBdatabaseTaxonomicClassification.xlsx: Taxonomic classification of the final MAGs conducted by applying GTDB-tk (v1.4.0) based on the GTDB Release 202 (1 file).Table3-ViralPopulationQualitySummary.xlsx: Summary of the completeness and quality of the identified viral populations (1 file). Table4-ViralPopulationTaxonomy.xlsx: Taxonomic classification of viral populations (1 file).File1-PRE_archaea.trimmed.concat.alignment & File2-PRE_bacteria.trimmed.concat.alignment: The concatenated alignment for further phylogenomic analysis (2 files).File3-PRE_archaea.trimmed.concat.newick & File4-PRE_bacteria.trimmed.concat.newick: The genome trees (2 files). File5-PRE_archaea.tree.iTOL.labels.txt & File6-PRE_bacteria.tree.iTOL.labels.txt: The iTOL annotation file of the genome trees (2 files).

项目描述：针对典型亚热带区域珠江口（Pearl River Estuary, PRE）表层水体中的微生物与病毒群落开展深度宏基因组测序。
数据描述：本数据集包含基于PRE微生物宏基因组数据生成的组装重叠群、宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）、病毒样重叠群及种群相关数据，具体如下：
1. PRET1608S??F00_idba-ud_final.fna.gz：来自病毒组（<0.2 μm）的重叠群序列，共5个文件。
2. PRET1608S??F0{2/7}_megahit_final.fna.gz：来自细胞宏基因组（0.2~0.7 μm与0.7~2.7 μm组分）的重叠群序列，共10个文件。
3. PRET1608S??F0{2/7}_MAGs.tar.gz：各宏基因组中完整性≥50%且污染率≤10%的MAGs。
4. PRE_all_dereplicated_MAGs.tar.gz：1205个去冗余原核基因组，均满足完整性≥50%且污染率≤10%的标准。
5. PRE_viral_contigs.fasta：从PRE三个粒径组分的重叠群中鉴定得到的推定病毒重叠群，共1个文件。
6. PRE_viral_contigs_95-80.fna：基于95%核苷酸一致性与80%基因组覆盖度标准构建的病毒种群序列，共1个文件。
7. Table1-SingleCopyMarkers.xlsx：分别包含122个古菌单拷贝标记蛋白与120个细菌单拷贝标记蛋白的信息，用于分别构建古菌与细菌的最大似然系统发育树，共1个文件。
8. Table2-MAGsGTDBdatabaseTaxonomicClassification.xlsx：基于GTDB Release 202版本，通过GTDB-tk（v1.4.0）对最终MAGs进行分类注释的结果文件，共1个文件。
9. Table3-ViralPopulationQualitySummary.xlsx：已鉴定病毒种群的完整性与质量统计结果文件，共1个文件。
10. Table4-ViralPopulationTaxonomy.xlsx：病毒种群的分类注释结果文件，共1个文件。
11. File1-PRE_archaea.trimmed.concat.alignment 与 File2-PRE_bacteria.trimmed.concat.alignment：用于后续系统基因组学分析的串联比对序列文件，共2个文件。
12. File3-PRE_archaea.trimmed.concat.newick 与 File4-PRE_bacteria.trimmed.concat.newick：基因组系统发育树文件，共2个文件。
13. File5-PRE_archaea.tree.iTOL.labels.txt 与 File6-PRE_bacteria.tree.iTOL.labels.txt：基因组系统发育树的iTOL注释文件，共2个文件。