Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P. R. China.
Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, P. R. China.
BMC Genomics. 2021 Apr 23;22(1):298. doi: 10.1186/s12864-021-07598-y.
Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes.
Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries.
Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
叶绿体是植物和藻类中重要的半自主细胞器。与高等植物不同，绿藻谱系的叶绿体基因组在组织和表达上都有明显的特征。尽管高等植物和几种藻类模式物种的叶绿体基因组结构已得到广泛研究，但对绿藻叶绿体编码基因的转录特征知之甚少。
基于全长 cDNA（Iso-Seq）测序，我们在绿藻 Caulerpa lentillifera 中鉴定出广泛共转录的多顺反子转录单元（PTUs）。除了来自同一途径的基因簇外，我们还鉴定了一系列多达九个基因的 PTUs，其在质体中的功能尚不清楚。RNA 数据还使我们能够进一步确认广泛表达的断裂基因和保守开放阅读框，这是绿藻叶绿体基因组的两个重要特征。此外，还发现了一种特定于 C. lentillifera 的新断裂基因，这可能代表质体基因组中最近的基因断裂事件。利用新注释的外显子-内含子边界信息，大大改进了硅藻类系的基因结构注释。我们的数据还揭示了一种非典型的 II 型内含子，其二级结构异常，内含子 ORF 缺乏已知的剪接或迁移结构域。这些广泛存在的内含子在其基因中具有保守的位置，尽管缺乏明确的共识内含子边界，但它们的切除却是精确的。
我们的研究填补了绿藻叶绿体基因组组织和转录方面的重要知识空白，为藻类叶绿体基因组中多顺反子转录物、独立 ORF 和断裂基因的表达提供了新的见解。此外，我们揭示了一种 Bryopsidales 中具有独特特征和保守位置的不寻常类型的 II 型内含子。我们的数据丰富了对叶绿体内含子结构的认识，并突出了未被表征的基因簇，这些基因簇可能在质体中发挥重要作用。
