Abstract
Genes with similar or related functions in chloroplasts are often arranged in close proximity, forming clusters on chromosomes. These clusters are transcribed coordinated to facilitate the expression of genes with specific function. Our previous study revealed a significant negative correlation between the chloroplast gene expression level of the rare medicinal fern Ophioglossum vulgatum and its evolutionary rates as well as selection pressure. Therefore, in this study, we employed a combination of SMRT and Illumina sequencing technology to analyze the full-length transcriptome sequencing of O. vulgatum for the first time. In particular, we experimentally identified gene clusters based on transcriptome data and investigated the effects of chloroplast gene clustering on expression and evolutionary patterns. The results revealed that the total sequenced data volume of the full-length transcriptome of O. vulgatum amounted to 71,950,652,163 bp, and 110 chloroplast genes received transcript coverage. Nine different types of gene clusters were experimentally identified in their transcripts. The chloroplast cluster genes may cause a decrease in non-synonymous substitution rate and selection pressure, as well as a reduction in transversion rate, transition rate, and their ratio. While expression levels of chloroplast cluster genes in leaf, sporangium, and stem would be relatively elevated. The Mann–Whitney U test indicated statistically significant in the selection pressure, sporangia and leaves groups (P < 0.05). We have contributed novel full-length transcriptome data resources for ferns, presenting new evidence on the effects of chloroplast gene clustering on expression land evolutionary patterns, and offering new theoretical support for transgenic research through gene clustering.
Key message
The clustering of chloroplast genes in Ophioglossum vulgatum demonstrates a tendency towards elevated expression levels in sporangium, leaf, and stem, while exhibiting a decline in evolutionary rates and selection pressure.
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Data availability
The full-length transcriptome data were deposited in NCBI Sequence Read Archive (SRA) at (https://www.ncbi.nlm.nih.gov/bioproject), the Accession Number is PRJNA856114.
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This work was supported by the National Natural Science Foundation of China (31872670 and 32071781), Guangdong Basic and Applied Basic Research Foundation (2021A1515010911), Science and Technology Projects in Guangzhou (202206010107), and Project of Department of Science and Technology of Shenzhen City, Guangdong, China (JCYJ20190813172001780 and JCYJ20210324141000001).
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TW and YS conceived and designed the research. JH and YL contributed to the genome sequencing. JH, YL, and JP analyzed the data. JH drew the maps and wrote the manuscript. TW and YS revised the manuscript. All authors approved the final version of the article.
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Hao, J., Liang, Y., Ping, J. et al. Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns. Plant Mol Biol 114, 31 (2024). https://doi.org/10.1007/s11103-024-01423-2
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DOI: https://doi.org/10.1007/s11103-024-01423-2