Abstract
Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic information, especially for species with complex genomes. Artemisia annua L. is the only commercial resource of artemisinin production though the content of artemisinin is still to be improved. Genome-based genetic modification and breeding are useful strategies to boost artemisinin content and therefore, ensure the supply of artemisinin and reduce costs, but better gene annotation is urgently needed. In this study, we manually corrected the newly released genome annotation of A. annua using second- and third-generation transcriptome data. We found that incorrect gene information may lead to differences in structural, functional, and expression levels compared to the original expectations. We also identified alternative splicing events and found that genome annotation information impacted identifying alternative splicing genes. We further demonstrated that genome annotation information and alternative splicing could affect gene expression estimation and gene function prediction. Finally, we provided a valuable version of A. annua genome annotation and demonstrated the importance of gene annotation in future research.
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Data availability
The raw sequencing datasets of A. annua were downloaded from the NCBI Sequence Read Archive under the accession number PRJNA752933. The genome data were downloaded from NCBI under the accession number PRJNA416223 and http://www.gpgenome.com/species/92. The corrected genome annotation file can be downloaded from https://github.com/liuzy2008/Artemisia_annua_annotation2023.
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Acknowledgements
We appreciate Dr. Chengjie Chen's support in using IGV-GSAman during the research process.
Funding
This work is supported by the National Key Research and Development Program (2019YFE0108700, China), the National Natural Science Foundation of China (U1812403-1), Scientific Research Project of Hainan Academician Innovation Platform (SQ2021PTZ0052; YSPTZX202137).
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SC, LL supervised the study. LL, ZL, and ZS collected the data. YD, ZS, ZB, ZY, YL, HZ, RY, and SK manually corrected the genome annotation. ZL and YD analyzed the data. LX and DQ provided all plant materials. LX designed all validation experiments. BC and YS helped conduct the verification experiment. ZL, YD, ZS, LX, HW, and BC wrote the manuscript.
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Liu, Z., Du, Y., Sun, Z. et al. Manual correction of genome annotation improved alternative splicing identification of Artemisia annua. Planta 258, 83 (2023). https://doi.org/10.1007/s00425-023-04237-6
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DOI: https://doi.org/10.1007/s00425-023-04237-6