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. 2023 Feb 9;13(2):jkac329.
doi: 10.1093/g3journal/jkac329.

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma

Kenta Shirasawa  1 , Ryohei Arimoto  2 , Hideki Hirakawa  1 , Motoyuki Ishimori  3 , Andrea Ghelfi  1   4 , Masami Miyasaka  5 , Makoto Endo  2 , Saneyuki Kawabata  6 , Sachiko N Isobe  1
Affiliations

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma

Kenta Shirasawa et al. G3 (Bethesda). .

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.

Keywords: Eustoma grandiflorum; gene prediction; genetic diversity; genome assembly.

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Conflict of interest statement

Conflicts of interest The authors declare no conflicts of interest associated with this manuscript.

Figures

Fig. 1.
Fig. 1.
Correlation between physical and genetic distances on the Eustoma genome. The genetic distances were calculated from the 10B-581 F2 linkage map.
Fig. 2.
Fig. 2.
Comparative and phylogenetic analyses with other plant species at the gene level. a) Number of gene clusters created with genes of E. grandiflorum (Ev), G. dahurica (Gd), O. pumila (Op), c) canephora (Cc), V. vinifera (Vv), and A. thaliana (At). b) A phylogenetic tree of 1,729 common single-copy genes of the 6 plant species. c) Distribution of Ks values of orthologous gene pairs in E. grandiflorum and the other 5 species.
See this image and copyright information in PMC

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