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Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data

文献类型： 外文期刊

作者： Zou, Xiaoxiao 1 ; Verbruggen, Heroen 3 ; Li, Tianjingwei 1 ; Zhu, Jun 1 ; Chen, Zou 1 ; He, Henqi 1 ; Bao, Shixiang 1 ; S 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Hainan Acad Trop Agr Resource, Inst Trop Biosci & Biotechnol, Haikou 571101, Hainan, Peoples R China

2.Hainan Prov Key Lab Funct Components Res & Utilil, Haikou 571101, Hainan, Peoples R China

3.Univ Melbourne, Sch BioSci, Parkville, Vic 3010, Australia

4.Chinese Acad Trop Agr Sci, Environm & Plant Protect Inst, Haikou 571101, Hainan, Peoples R China

关键词： Chloroplast genome; Polycistronic transcripts; Gene fragmentation; Freestanding ORF; Group II intron; Siphonous algae; PacBio; Iso-seq

期刊名称：BMC GENOMICS （ 影响因子：3.594； 五年影响因子：4.093 ）

ISSN： 1471-2164

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background 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. Results 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. Conclusion 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.

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