Complete mitochondrial genome of the branching octocoral Paramuricea grayi (Johnson, 1861), phylogenetic relationships and divergence analysis

The present data files are supporting data to the manuscript submission to <em>Mitochondrial DNA Part B</em> announcing the mitochondrial genome sequence of the octocoral <em>Paramuricea grayi</em>. The fasta files included contain the complete/partial mitochondrial genome sequences of multiple specimens of <em>Paramuricea grayi, Paramuricea clavata </em>and <em>Paramuricea biscaya a</em>assembled from RNA-seq data. The mitogenomes were assembled with MITGARD (<strong>Mit</strong>ochondrial <strong>G</strong>enome <strong>A</strong>ssembly from <strong>R</strong>NA-seq <strong>D</strong>ata) (Nachtigall et al. 2021) using default parameters and the reference mitogenome of<em> P. clavata</em> as bait (Genbank Accession: NC_034749). The RNA-seq read data for <em>P. clavata</em> and <em>P. grayi</em> were obtained from a previous study by our teams (Coelho et al. 2022), which has been submited for publication in Molecular Ecology (Authorea pre-print: DOI:10.22541/au.165544523.32209087/v1). The raw read data can be retrieved from NCBI's Sequence Read Archive (SRA) under BioProject ID PRJNA847883. The <em>P. biscaya</em> raw data are from a previous study by DeLeo et al. 2018 and can be accessed in SRA under BioProject ID PRJNA481028. The top quality assemblies for <em>P. grayi</em> (isolate=BAL_C3) and <em>P. clavata</em> (isolate=VAC_T1) have been submitted to Genbank under accessions OP205061 and OP205062, respectively. <br> <strong>References</strong> Coelho MAG, Pearson G, Boavida J, Paulo D, Aurelle D, Arnaud-Haond S, Gómez-Gras D, Bensoussan N, López- Sendino P, Cerrano C, Kipson S, Bakran-Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão E, Ledoux J-B (2022) Not out of the Mediterranean: Atlantic populations of the gorgonian <em>Paramuricea clavata </em>are a separate sister species under further lineage diversification. Authorea. DOI:10.22541/au.165544523.32209087/v1 <br> DeLeo DM, Herrera S, Lengyel SD, Quattrini AM, Kulathinal RJ, Cordes EE. 2018. Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill. Mol Ecol. 27:4066–4077. <br> Nachtigall PG, Grazziotin FG, Junqueira-De-Azevedo ILM. 2021. MITGARD: An automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data. Brief Bioinform. 22(5):1-15.

本数据集文件为提交至《Mitochondrial DNA Part B》手稿的配套补充数据，该手稿报道了八放珊瑚（octocoral）灰原鞭柳珊瑚（Paramuricea grayi）的线粒体基因组序列。本次提供的FASTA格式文件，包含了从RNA测序（RNA-seq）数据组装得到的多份灰原鞭柳珊瑚（Paramuricea grayi）、棒状原鞭柳珊瑚（Paramuricea clavata）及比氏原鞭柳珊瑚（Paramuricea biscaya）的完整/部分线粒体基因组序列。本研究依托MITGARD（基于RNA-seq数据的线粒体基因组组装工具，Mitochondrial Genome Assembly from RNA-seq Data）（Nachtigall等，2021），采用默认参数，以棒状原鞭柳珊瑚的线粒体基因组作为参考诱饵序列（GenBank登录号：NC_034749）完成线粒体基因组组装。棒状原鞭柳珊瑚与灰原鞭柳珊瑚的RNA-seq测序读段数据取自本团队此前发表的研究（Coelho等，2022），该研究已提交至《Molecular Ecology》期刊预印本（Authorea预印本：DOI:10.22541/au.165544523.32209087/v1）。原始读段数据可通过美国国家生物技术信息中心（NCBI）序列读取归档（Sequence Read Archive, SRA）数据库获取，对应的BioProject编号为PRJNA847883。而比氏原鞭柳珊瑚的原始读段数据取自DeLeo等2018年的研究，可通过SRA数据库的BioProject编号PRJNA481028获取。灰原鞭柳珊瑚（分离株BAL_C3）与棒状原鞭柳珊瑚（分离株VAC_T1）的高质量组装序列已提交至GenBank，登录号分别为OP205061与OP205062。

**参考文献**
1. Coelho MAG, Pearson G, Boavida J, Paulo D, Aurelle D, Arnaud-Haond S, Gómez-Gras D, Bensoussan N, López-Sendino P, Cerrano C, Kipson S, Bakran-Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão E, Ledoux J-B (2022) 并非仅分布于地中海：大西洋的棒状原鞭柳珊瑚种群为独立分化的姊妹类群。Authorea预印本. DOI:10.22541/au.165544523.32209087/v1
2. DeLeo DM, Herrera S, Lengyel SD, Quattrini AM, Kulathinal RJ, Cordes EE. 2018. 基因表达谱分析揭示深海珊瑚对深水地平线漏油事件的响应. 分子生态学（Molecular Ecology）. 27:4066–4077.
3. Nachtigall PG, Grazziotin FG, Junqueira-De-Azevedo ILM. 2021. MITGARD：基于RNA-seq数据组装真核生物线粒体基因组的自动化流程. Brief Bioinform. 22(5):1-15.