Comparative Genomic Analysis of Chrysanthemum

The translated protein sequences of CSE_r1.1_cds were clustered by OrthoMCL with those of A. thaliana (Araport11, https://www.araport.org/data/araport11/), S. lycopersicum (tomato, ITAG3.2),¹⁷ (link)Lactuca sativa (lettuce, Lsativa_467_v5, http://lgr.genomecenter.ucdavis.edu/)²³ (link) and Helianthus annuus (sunflower, Ha412v1r1_port_v1.0)²⁴ (link) with the parameters c = 0.6 and aL = 0.9. The phylogenetic analysis was performed by MEGA 7.0.9 beta and TIMETREE based on the single copy genes conserved in C. seticuspe and the four species. The divergence time of 104 MYA between A. thaliana and S. lycopersicum was used for calibration. The published sequence read archive (SRA) transcripts for six cultivated chrysanthemum (C. × morifolium) varieties were mapped onto CSE_r1.0 by TopHat v2.1.1 (Supplementary Table S1b) in order to investigate the mapped ratios and identify variants. Variants were called based on the mapping result using SAMtools 0.1.19 and subsequently filtered using VarScan 2.3. SNP effects on gene function were predicted by using SnpEff ver.4.0.

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Hirakawa H., Sumitomo K., Hisamatsu T., Nagano S., Shirasawa K., Higuchi Y., Kusaba M., Koshioka M., Nakano Y., Yagi M., Yamaguchi H., Taniguchi K., Nakano M, & Isobe S.N. (2019). De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 26(3), 195-203.

Publication 2019

Chrysanthemum Gene function Genes Lettuce Mega 9 Protein sequences Sunflower Tomato

Corresponding Organization : Kazusa DNA Research Institute

Other organizations : Institute of Vegetable and Floriculture Science, Forestry and Forest Products Research Institute, The University of Tokyo, Hiroshima University, Nihon University

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Variable analysis

independent variables

The translated protein sequences of CSE_r1.1_cds were clustered by OrthoMCL with those of A. thaliana (Araport11), S. lycopersicum (tomato, ITAG3.2), Lactuca sativa (lettuce, Lsativa_467_v5), and Helianthus annuus (sunflower, Ha412v1r1_port_v1.0)
The parameters c = 0.6 and aL = 0.9 were used for the OrthoMCL clustering

dependent variables

The phylogenetic analysis was performed by MEGA 7.0.9 beta and TIMETREE based on the single copy genes conserved in C. seticuspe and the four species
The published sequence read archive (SRA) transcripts for six cultivated chrysanthemum (C. × morifolium) varieties were mapped onto CSE_r1.0 by TopHat v2.1.1 in order to investigate the mapped ratios and identify variants
Variants were called based on the mapping result using SAMtools 0.1.19 and subsequently filtered using VarScan 2.3
SNP effects on gene function were predicted by using SnpEff ver.4.0

control variables

The divergence time of 104 MYA between A. thaliana and S. lycopersicum was used for calibration

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