Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization
Abstract Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editin...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-10-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-22589-z |
| _version_ | 1811335059458752512 |
|---|---|
| author | Mitsuko Kishi-Kaboshi Tsuyoshi Tanaka Katsutomo Sasaki Naonobu Noda Ryutaro Aida |
| author_facet | Mitsuko Kishi-Kaboshi Tsuyoshi Tanaka Katsutomo Sasaki Naonobu Noda Ryutaro Aida |
| author_sort | Mitsuko Kishi-Kaboshi |
| collection | DOAJ |
| description | Abstract Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained ‘Sei Arabella’ transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome. |
| first_indexed | 2024-04-13T17:18:24Z |
| format | Article |
| id | doaj.art-50fc2d284dcb419da6508ad64a0dab16 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-13T17:18:24Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-50fc2d284dcb419da6508ad64a0dab162022-12-22T02:38:04ZengNature PortfolioScientific Reports2045-23222022-10-0112111510.1038/s41598-022-22589-zCombination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorizationMitsuko Kishi-Kaboshi0Tsuyoshi Tanaka1Katsutomo Sasaki2Naonobu Noda3Ryutaro Aida4Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO)Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO)Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO)Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO)Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO)Abstract Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained ‘Sei Arabella’ transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome.https://doi.org/10.1038/s41598-022-22589-z |
| spellingShingle | Mitsuko Kishi-Kaboshi Tsuyoshi Tanaka Katsutomo Sasaki Naonobu Noda Ryutaro Aida Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization Scientific Reports |
| title | Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization |
| title_full | Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization |
| title_fullStr | Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization |
| title_full_unstemmed | Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization |
| title_short | Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization |
| title_sort | combination of long read and short read sequencing provides comprehensive transcriptome and new insight for chrysanthemum morifolium ray floret colorization |
| url | https://doi.org/10.1038/s41598-022-22589-z |
| work_keys_str_mv | AT mitsukokishikaboshi combinationoflongreadandshortreadsequencingprovidescomprehensivetranscriptomeandnewinsightforchrysanthemummorifoliumrayfloretcolorization AT tsuyoshitanaka combinationoflongreadandshortreadsequencingprovidescomprehensivetranscriptomeandnewinsightforchrysanthemummorifoliumrayfloretcolorization AT katsutomosasaki combinationoflongreadandshortreadsequencingprovidescomprehensivetranscriptomeandnewinsightforchrysanthemummorifoliumrayfloretcolorization AT naonobunoda combinationoflongreadandshortreadsequencingprovidescomprehensivetranscriptomeandnewinsightforchrysanthemummorifoliumrayfloretcolorization AT ryutaroaida combinationoflongreadandshortreadsequencingprovidescomprehensivetranscriptomeandnewinsightforchrysanthemummorifoliumrayfloretcolorization |