AUTHOR=He Ziyan , Chen Yang , Wang Yichao , Liu Kuiyan , Xu Qing , Li Yang , Chen Nansheng 

TITLE=Comparative Analysis of Pseudo-nitzschia Chloroplast Genomes Revealed Extensive Inverted Region Variation and Pseudo-nitzschia Speciation

JOURNAL=Frontiers in Marine Science

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2022.784579

DOI=10.3389/fmars.2022.784579

ISSN=2296-7745

ABSTRACT=<p><italic>Pseudo-nitzschia</italic> 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 <italic>Pseudo-nitzschia</italic> 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 <italic>Pseudo‐nitzschia</italic>, among which cpDNAs of eight <italic>Pseudo-nitzschia</italic> species were reported for the first time. The sizes of these <italic>Pseudo-nitzschia</italic> 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 <italic>psaE</italic> in cpDNAs of all <italic>Pseudo-nitzschia</italic> species except that of <italic>P. americana</italic>, and the selective loss of <italic>rpl36</italic> in <italic>P. hainanensis</italic>. Phylogenetic analysis showed that all <italic>Pseudo-nitzschia</italic> strains were grouped into two clades, with clade 1 containing cpDNAs of <italic>P. multiseries</italic>, <italic>P. pungens</italic>, <italic>P. multistriata</italic>, and <italic>P. americana</italic>, and clade 2 containing cpDNAs of <italic>P. hainanensis</italic>, <italic>P. cuspidata</italic>, <italic>Pseudo-nitzschia</italic> sp. CNS00097, <italic>P. delicatissima</italic>, and <italic>P. micropora</italic>. The small size of the <italic>P. americana</italic> cpDNA was primarily due to its shortened inverted repeat (IR) regions. While <italic>psaA</italic> and <italic>psaB</italic> were found in the IR regions of cpDNAs of other eight species, these two genes were found outside of the IR regions of <italic>P. americana</italic> cpDNA. In contrast, <italic>P. hainanensis</italic> 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 <italic>Pseudo-nitzschia</italic> cpDNAs exhibited high nucleotide diversity (Pi) values, suggesting that these regions may be used as molecular markers for distinguishing different <italic>Pseudo-nitzschia</italic> species with high resolution and high specificity. Phylogenetic analysis of the divergence of nine <italic>Pseudo-nitzschia</italic> 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 <italic>Pseudo-nitzschia</italic> species.</p>