Assembled genomes of sulfur-oxidizing symbiotic bacteria in the gut of polychaetes

This study presents 12 assembled genomes of sulfur-oxidizing symbiotic bacteria associated with the gut tissues of deep-sea polychaetes. The data originated from specimens collected at two sites. One is from the Kairei hydrothermal vent (70.04010°E, 25.32048°S) at 2,421 m in the Central Indian Ridge by the manned submersible Deep-Sea Yongshi during R/V Tansuoyihao research cruise TS10-03 (February 2019), and the other is from the nature whale fall (97.26709 E, 32.79041°S) at 5,660m in the Diamantina Trench by the manned submersible Fendouzhe during R/V Tansuoyihao research cruise TS29-03 (January 2023). Collected gut tissue samples were immediately dissected on deck and preserved at -80°C until subsequent DNA extraction.Metagenomic DNA was extracted using the PowerSoil® DNA Isolation Kit. Sequencing libraries were prepared following standard protocols and sequenced on PE250 sequencing on the Illumina platform. Metagenomic raw data were trimmed and filtered by Fastp with default settings. The data were further processed with FastUniq to remove duplicated reads. Clean data were separately assembled using both SPAdes with the recommended settings for metagenomes and MEGAHIT with default settings. Assembled datasets were subjected to MetaWRAP v1.2.1 for genome binning with default settings. These retrieved MAGs were then de-replicated together using dRep, which resulted in 12 Sulfurovaceae MAGs.The final released dataset comprises 12 MAGs of sulfur-oxidizing symbionts, all with completeness higher than 50% and contamination lower than 10%.The nucleotide sequences of each MAG are provided in separate standard FASTA format files (.fna). Corresponding predicted protein-coding sequence files (.faa) and functional annotation files (.gff) are also provided. All relevant files (including the core data table and individual genome sequence and annotation files) have been consolidated and compressed into an archive named "Polychaetes_symbiont_MAGs_dataset.zip". These data provide a valuable genomic resource for in-depth studies of host-microbe interaction mechanisms in deep-sea chemosynthetic ecosystems.

本研究报道了12株与深海多毛类动物肠道组织共生的硫氧化共生菌的组装基因组。该数据集的样本采自两个采样点：其一为中央印度洋脊2421米水深的Kairei热液喷口（东经70.04010°，南纬25.32048°），由载人深潜器“深海勇士号”（Deep-Sea Yongshi）在“探索一号”（R/V Tansuoyihao）科考航次TS10-03（2019年2月）期间采集；其二为迪亚曼蒂纳海沟5660米水深的自然鲸落（东经97.26709，南纬32.79041°），由载人深潜器“奋斗者号”（Fendouzhe）在“探索一号”科考航次TS29-03（2023年1月）期间采集。采集的肠道组织样本即刻在甲板上完成解剖，并保存于-80℃直至后续DNA提取。采用PowerSoil® DNA Isolation Kit进行宏基因组DNA提取。按照标准流程构建测序文库，并在Illumina平台上采用PE250测序模式完成测序。使用Fastp软件以默认参数对宏基因组原始数据进行修剪与质控过滤，再通过FastUniq去除重复读段。清洁数据分别采用适配宏基因组分析的推荐参数SPAdes软件，以及默认参数的MEGAHIT软件完成基因组组装。采用MetaWRAP v1.2.1软件以默认参数对组装得到的数据集进行基因组分箱，随后通过dRep工具对获取的宏基因组组装基因组（Metagenome-assembled Genome，MAG）进行去冗余，最终得到12株硫杆菌科（Sulfurovaceae）的MAGs。最终发布的数据集包含12株硫氧化共生菌的MAGs，所有MAG的完整度均高于50%，污染度低于10%。每个MAG的核苷酸序列以独立的标准FASTA格式文件（.fna）提供，同时附带对应的预测蛋白质编码序列文件（.faa）与功能注释文件（.gff）。所有相关文件（包括核心数据表、单基因组序列及注释文件）已整合并压缩为名为“Polychaetes_symbiont_MAGs_dataset.zip”的归档文件。本数据集为深海化能合成生态系统中宿主-微生物互作机制的深入研究提供了宝贵的基因组资源。