Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.硅藻（diatom）是藻类中物种多样性最为丰富的类群，但其叶绿体基因组（chloroplast genome）的多样性，尤其是同一属内的多样性，尚未得到充分记录。本研究报道了Halamphora属的3个叶绿体基因组，涉及H. americana、H. calidilacuna及H. coffeaeformis三个物种，该属是首个拥有多个物种叶绿体基因组测序数据的羽纹硅藻（pennate diatom）属。Halamphora属的叶绿体基因组大小介于约120至150千碱基对（kb）之间，属内基因组大小差异可达24%。基因组大小的差异主要源于反向重复区（inverted repeat region）长度、基因间区（intergenic region）长度的变化，以及疑似编码尚未被鉴定蛋白的开放阅读框（open reading frame，ORF）的存在与否存在变异。三个物种共拥有161个核心基因特征，但在两个基因的存在情况上存在差异：serC与tyrC，二者分别来自外源且起源未知。将本研究数据与已发表的3个隶属于海链藻目Thalassiosirales的非羽纹硅藻类小环藻属（Cyclotella）的叶绿体基因组进行比对后发现，相较于其他类群，Halamphora属的叶绿体基因组发生了大量重排，且属内同样存在基因组变异。最后，将Halamphora属的叶绿体基因组与陆生植物的叶绿体基因组进行比对后发现，该属硅藻的叶绿体基因组进化速率至少是陆生植物的4至7倍。此类研究能够为硅藻叶绿体演化研究提供更深入的认知，同时也为后续分析提供了宝贵的遗传资源。