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Shirasawa K, Arimoto R, Hirakawa H, Ishimori M, Ghelfi A, Miyasaka M, Endo M, Kawabata S, Isobe SN. Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma. G3 (BETHESDA, MD.) 2022; 13:6931796. [PMID: 36529465 PMCID: PMC9911058 DOI: 10.1093/g3journal/jkac329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
Eustoma grandiflorum (Raf.) Shinn. is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and is an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum genome sequences by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. Thirty-six pseudomolecules and 64 unplaced scaffolds were created, with a total length of 1,324.8 Mb. A total of 36,619 genes were predicted on the genome as high-confidence genes. A comparison of genome structure between E. grandiflorum and C. canephora or O. pumila suggested whole-genome duplication after the divergence between the families Gentianaceae and Rubiaceae. Phylogenetic analysis with single-copy genes suggested that the divergence time between Gentianaceae and Rubiaceae was 74.94 MYA. Genetic diversity analysis was performed for nine commercial E. grandiflorum varieties bred in Japan, from which 254,205 variants were identified. This first report on the construction of a reference genome sequence in the genus Eustoma is expected to contribute to genetic and genomic studies in this genus and in the family Gentianaceae.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Ryohei Arimoto
- Takii & Co., Ltd., Hari 1360, Konan, Shiga 520-3231, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, 2-6-7, Kisarazu, Chiba 292-0818, Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Andrea Ghelfi
- Kazusa DNA Research Institute, Kazusa-Kamatari, 2-6-7, Kisarazu, Chiba 292-0818, Japan,Bioinformation and DDBJ Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Masami Miyasaka
- Nagano Vegetable and Ornamental Crops Experiment Station, 1066-1 Soga, Shiojiri City, Nagano 399-6461, Japan
| | - Makoto Endo
- Takii & Co., Ltd., Hari 1360, Konan, Shiga 520-3231, Japan
| | - Saneyuki Kawabata
- Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Midori, Nishitokyo-Shi, Tokyo 18-0002, Japan
| | - Sachiko N Isobe
- Corresponding author: Kazusa DNA Research Institute, Kazusa-Kamatari, 2-6-7, Kisarazu, Chiba 292-081, Japan.
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