ProSynTaxDB: Prochlorococcus and Synechococcus Taxonomy Database

INTRODUCTION:

Understanding the distribution of the abundant and closely related picocyanobacteria, Prochlorococcus and Synechococcus, is essential for understanding marine ecosystems. These organisms are highly diverse, making the accurate classification of clusters/clades/grades within each genus challenging. As a result, Prochlorococcus and Synechococcus populations are often characterized as a single strain, concealing the well-documented fine-scale niche partitioning within these groups (Johnson, et al., 2006, Hunter-Cevera, et al., 2016, Larkin, et al., 2016, Kent, et al., 2019, Thompson, et al., 2021, Ustick et al., 2023). Here, we introduce ProSynTaxDB and its associated workflow, designed to significantly improve metagenomic classification of Prochlorococcus and Synechococcus using a substantial amount of high-quality genomic reference data collected over the past decade and from this study. ProSynTaxDB includes 1,260 single-cell amplified genomes, high-quality draft cultured genomes, and unpublished closed genomes, featuring new closed circular assemblies for 40 Prochlorococcus, 12 Synechococcus, and 10 marine heterotrophic bacterial strains. This includes 21 Prochlorococcus genomes that were previously partially assembled (Biller et al., 2014) and 16 genomes from unpublished isolates. Additionally, the database includes 27,799 genomes of marine heterotrophic bacteria, archaea, and viruses to assess communities surrounding Prochlorococcus and Synechococcus. ProSynTaxDB and the accompanying workflow can accurately identify clades in metagenomic samples containing at least 0.60% Prochlorococcus reads or 0.09% Synechococcus reads, thereby improving our understanding of these picocyanobacteria in low-abundance regions.

Github to the associated workflow: https://github.com/jamesm224/ProSynTaxDB-workflow

FILE DESCRIPTION: 

ProSynTaxDB_genomes.tsv

Table of genomes included in the ProSynTaxDB and their associated metadata (Data Citation 1). Data fields are as follows:

organism: The name of the organism recorded in NCBI when available. For genomes/organisms obtained from sources other than NCBI, the organism name is provided in NCBI format

genome_short_name: The genome name used in the ProSynTaxDB

domain: Bacteria, Archaea, Eukarya, or Virus

genus: The genus of the organism in NCBI

clade: The major cluster/clade/grade of Prochlorococcus or Synechococcus based on phylogenetic reconstruction using a concatenated alignment of proteins encoded by single-copy core genes

NCBI_BioProject: The NCBI BioProject accession number associated with the organism, when available

NCBI_BioSample: The NCBI BioSample accession number associated with the organism, when available

NCBI_GenBank: The NCBI GenBank accession number associated with the genome sequence data, when available

IMG_Genome_ID: The IMG Genome ID accession number, when available, associated with the genome/organism in the Joint Genome Institute’s (JGI) Integrated Microbial Genomes (IMG) repository. The IMG Genome ID is synonymous with the IMG Taxon ID

ProSynTaxDB_names.dmp

Names taxonomy file for use with the ProSynTaxDB.

ProSynTaxDB_nodes.dmp

Nodes taxonomy file for use with the ProSynTaxDB.

ProSynTaxDB.fmi

Index file containing contents of ProSynTaxDB_v1.faa for use with ProSynTaxDB.

CyCOG6.dmnd

Database containing orthologous groups of proteins used in the cluster/clade/grade normalization step. 

ProSynTaxDB.faa 

File containing protein sequences used by Kaiju for classification of reads. Each protein sequence contains a header starting with “>”. 

average_cycog_length.csv

Comma separated file containing the average length for each protein sequence used in the normalization step. Data fields are as follows: cycog: name for single-copy core gene

mean_AA_length: the average length of amino acids in the protein sequence of the gene

ProSynTaxDB-workflow_benchmarking_genomes.tsv

This tab-delimited file contains a list of subsetted genomes used in each benchmarking experiment done in the Technical Validation section. Data fields are as follows:

Experiment Name: name of benchmarking experiment conducted

Subset ID: unique ID from the random genome subsetting 

Genome Name: name of genome used in benchmarking experiment 

ProSynTaxDB-workflow_benchmarking_composition.tsv

This tab-delimited file contains the taxon composition of all samples used in each benchmarking experiment done in the Technical Validation section. Data fields are as follows:

Experiment Name: name of benchmarking experiment conducted

Sample Name: unique sample name 

Percent Prochlorococcus: percent of reads in simulated sample originating from Prochlorococcus genomes 

Percent Synechococcus: percent of reads in simulated sample originating from Synechococcus genomes 

Percent Heterotroph: percent of reads in simulated sample originating from marine heterotrophic bacterial genomes 

Notes: additional information about the simulated sample

INTRODUCTION:

解析丰度颇高且亲缘关系紧密的微微型蓝细菌（picocyanobacteria）——原绿球藻（Prochlorococcus）与聚球藻（Synechococcus）的分布规律，对于理解海洋生态系统至关重要。这类微生物具有极高的多样性，这使得对每个属内的类群/进化枝/等级进行精准分类颇具挑战。因此，原绿球藻与聚球藻的种群常被笼统地归为单一菌株，这掩盖了这些类群中已有大量文献记载的精细生态位分化现象（Johnson等，2006；Hunter-Cevera等，2016；Larkin等，2016；Kent等，2019；Thompson等，2021；Ustick等，2023）。

在此，我们推出ProSynTaxDB及其配套分析流程，该工具依托近十年间积累及本研究新增的海量高质量基因组参考数据，旨在大幅提升原绿球藻与聚球藻的宏基因组（metagenomic）分类精度。ProSynTaxDB收录了1260个单细胞扩增基因组（single-cell amplified genomes）、高质量培养物草图基因组以及未公开的完成图基因组，其中包含40个原绿球藻、12个聚球藻以及10个海洋异养细菌菌株的全新闭合环状组装序列。其中包含21个此前仅完成部分组装的原绿球藻基因组（Biller等，2014）以及16个来自未公开分离株的基因组。

此外，该数据库还收录了27799个海洋异养细菌、古菌及病毒的基因组，用于解析原绿球藻与聚球藻的周边群落。ProSynTaxDB及其配套流程可在包含至少0.60%原绿球藻测序读段或0.09%聚球藻测序读段的宏基因组样本中精准识别进化枝，从而增进我们对低丰度区域中这些微微型蓝细菌的认知。

本配套分析流程的GitHub仓库地址：https://github.com/jamesm224/ProSynTaxDB-workflow

FILE DESCRIPTION:

ProSynTaxDB_genomes.tsv
ProSynTaxDB收录的基因组及其关联元数据表格（数据引文1）。各数据字段说明如下：
organism：若可获取，则为NCBI中记录的生物名称；若基因组/生物来自NCBI以外的数据源，则以NCBI格式提供生物名称。
genome_short_name：ProSynTaxDB中使用的基因组名称。
domain：所属域，包括细菌（Bacteria）、古菌（Archaea）、真核生物（Eukarya）或病毒（Virus）。
genus：NCBI中记录的生物所属属。
clade：基于单拷贝核心基因编码蛋白的串联联配序列进行系统发育重建得到的原绿球藻或聚球藻的主要类群/进化枝/等级。
NCBI_BioProject：若可获取，则为与该生物关联的NCBI BioProject登录号。
NCBI_BioSample：若可获取，则为与该生物关联的NCBI BioSample登录号。
NCBI_GenBank：若可获取，则为与该基因组序列数据关联的NCBI GenBank登录号。
IMG_Genome_ID：若可获取，则为联合基因组研究所（Joint Genome Institute, JGI）整合微生物基因组（Integrated Microbial Genomes, IMG）数据库中与该基因组/生物关联的IMG基因组ID登录号。IMG基因组ID与IMG分类群ID同义。

ProSynTaxDB_names.dmp
适用于ProSynTaxDB的分类学名称文件。

ProSynTaxDB_nodes.dmp
适用于ProSynTaxDB的分类学节点文件。

ProSynTaxDB.fmi
包含ProSynTaxDB_v1.faa内容的索引文件，供ProSynTaxDB使用。

CyCOG6.dmnd
包含用于类群/进化枝/等级标准化步骤的蛋白质直系同源簇的数据库。

ProSynTaxDB.faa
包含用于Kaiju进行读段分类的蛋白质序列的文件。每条蛋白质序列的标题以“>”开头。

average_cycog_length.csv
逗号分隔格式文件，包含标准化步骤中使用的各蛋白质序列的平均长度。各数据字段说明如下：
cycog：单拷贝核心基因的名称。
mean_AA_length：该基因蛋白质序列的氨基酸平均长度。

ProSynTaxDB-workflow_benchmarking_genomes.tsv
该制表符分隔文件包含了技术验证部分中各基准测试实验所用的基因组子集列表。各数据字段说明如下：
Experiment Name：所开展的基准测试实验名称。
Subset ID：随机基因组亚组的唯一标识符。
Genome Name：基准测试实验中所用的基因组名称。

ProSynTaxDB-workflow_benchmarking_composition.tsv
该制表符分隔文件包含了技术验证部分中各基准测试实验所用全部样本的分类组成。各数据字段说明如下：
Experiment Name：所开展的基准测试实验名称。
Sample Name：唯一的样本名称。
Percent Prochlorococcus：模拟样本中源自原绿球藻基因组的测序读段占比。
Percent Synechococcus：模拟样本中源自聚球藻基因组的测序读段占比。
Percent Heterotroph：模拟样本中源自海洋异养细菌基因组的测序读段占比。
Notes：关于该模拟样本的附加信息。