Table_8_Comparative Analysis of Pseudo-nitzschia Chloroplast Genomes Revealed Extensive Inverted Region Variation and Pseudo-nitzschia Speciation.xlsx

Pseudo-nitzschia is a species-rich genus where many species can induce harmful algae blooms (HABs) associated with the toxin domoic acid (DA) production. Despite the importance of Pseudo-nitzschia species to coastal environments, their genomic information is rather limited, hindering research on biodiversity and evolutionary analysis. In this study, we report full-length chloroplast genomes (cpDNAs) of nine Pseudo‐nitzschia, among which cpDNAs of eight Pseudo-nitzschia species were reported for the first time. The sizes of these Pseudo-nitzschia cpDNAs, which showed typical quadripartite structures, varied substantially, ranging from 116,546 bp to 158,840 bp in size. Comparative analysis revealed the loss of photosynthesis-related gene psaE in cpDNAs of all Pseudo-nitzschia species except that of P. americana, and the selective loss of rpl36 in P. hainanensis. Phylogenetic analysis showed that all Pseudo-nitzschia strains were grouped into two clades, with clade 1 containing cpDNAs of P. multiseries, P. pungens, P. multistriata, and P. americana, and clade 2 containing cpDNAs of P. hainanensis, P. cuspidata, Pseudo-nitzschia sp. CNS00097, P. delicatissima, and P. micropora. The small size of the P. americana cpDNA was primarily due to its shortened inverted repeat (IR) regions. While psaA and psaB were found in the IR regions of cpDNAs of other eight species, these two genes were found outside of the IR regions of P. americana cpDNA. In contrast, P. hainanensis had the largest size because of expansion of IR regions with each IR region containing 15 protein-coding genes (PCGs). Eleven genetic regions of these Pseudo-nitzschia cpDNAs exhibited high nucleotide diversity (Pi) values, suggesting that these regions may be used as molecular markers for distinguishing different Pseudo-nitzschia species with high resolution and high specificity. Phylogenetic analysis of the divergence of nine Pseudo-nitzschia species indicated that these species appeared at approximately 41 Mya. This study provides critical cpDNA resources for future research on the biodiversity and speciation of Pseudo-nitzschia species.

拟菱形藻属（Pseudo-nitzschia）是一个物种丰富的类群，其多数物种可引发与软骨藻酸（domoic acid, DA）合成相关的有害藻华（harmful algae blooms, HABs）。尽管拟菱形藻属物种对海岸生态系统至关重要，但目前其基因组信息仍较为匮乏，这阻碍了生物多样性与进化分析相关研究的开展。本研究报道了9株拟菱形藻的完整叶绿体基因组（chloroplast genomes, cpDNAs），其中8株拟菱形藻物种的叶绿体基因组为首次报道。这些拟菱形藻的叶绿体基因组均呈现典型的四分体结构，基因组大小差异显著，跨度介于116546 bp至158840 bp之间。比较基因组分析显示，除美洲拟菱形藻（P. americana）外，所有拟菱形藻物种的叶绿体基因组均丢失了光合相关基因psaE；而海南拟菱形藻（P. hainanensis）则选择性丢失了rpl36基因。系统发育分析表明，所有供试拟菱形藻菌株可分为两个演化支：支系1包含多列拟菱形藻（P. multiseries）、尖刺拟菱形藻（P. pungens）、多纹拟菱形藻（P. multistriata）以及美洲拟菱形藻的叶绿体基因组；支系2则包含海南拟菱形藻（P. hainanensis）、尖形拟菱形藻（P. cuspidata）、拟菱形藻未定种CNS00097（Pseudo-nitzschia sp. CNS00097）、细弱拟菱形藻（P. delicatissima）以及微拟菱形藻（P. micropora）的叶绿体基因组。美洲拟菱形藻的叶绿体基因组尺寸较小，主要源于其反向重复（inverted repeat, IR）区域发生了缩短。其余8个物种的叶绿体基因组中，psaA与psaB基因均位于反向重复区域内，而美洲拟菱形藻的这两个基因则位于反向重复区域之外。与之相反，海南拟菱形藻的叶绿体基因组尺寸最大，这源于其反向重复区域发生了扩张，每个反向重复区域均包含15个蛋白质编码基因（protein-coding genes, PCGs）。这些拟菱形藻的叶绿体基因组中共存在11个具有高核苷酸多样性（nucleotide diversity, Pi）的基因区域，提示这些区域可作为高分辨率、高特异性的分子标记，用于区分不同的拟菱形藻物种。对9株拟菱形藻物种分化时间的系统发育分析显示，该属物种的分化时间约为4100万年前（41 Mya）。本研究为后续拟菱形藻属物种的生物多样性与物种形成相关研究提供了关键的叶绿体基因组资源。