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Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants

Kim, Yong-Min, Kim, Seungill, Koo, Namjin, Shin, Ah-Young, Yeom, Seon-In, Seo, Eunyoung, Park, Seong-Jin, Kang, Won-Hee, Kim, Myung-Shin, Park, Jieun, Jang, Insu, Kim, Pan-Gyu, Byeon, Iksu, Kim, Min-Seo, Choi, JinHyuk, Ko, Gunhwan, Hwang, JiHye, Yang, Tae-Jin, Choi, Sang-Bong, Lee, Je Min, Lim, Ki-Byung, Lee, Jungho, Choi, Ik-Young, Park, Beom-Seok, Kwon, Suk-Yoon, Choi, Doil, Kim, Ryan W.·2016·DNA Research
DOI 10.1093/dnares/dsw049PMC PMC5381346
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Figure 1 Distribution of orthologous gene families of H. syriacus, G. raimondii, T. cacao, A. trichopoda and A. thaliana, from which 169,570 sequences were clustered into 9,076 groups. The number of clustered groups and genes in each species are shown on the left and center, and total gene numbers are shown on the right.
Figure 1 Distribution of orthologous gene families of H. syriacus, G. raimondii, T. cacao, A. trichopoda and A. thaliana, from which 169,570 sequences were clustered into 9,076 groups. The number of clustered groups and genes in each species are shown on the left and center, and total gene numbers are shown on the right.CC BY-NC · PubMed Central
Figure 2 Collinearity block detection and calculation of gene duplication times. (A) Collinearity blocks of the T. cacao genome were detected in G. raimondii and H. syriacus. (B) Calculation of divergence times of individual gene families. Circles and triangles indicate H. syriacus and G. raimondii, respectively, and shade boxes indicate each WGD. (C) Divergence time of Malvales plants. H. syriacus diverged from the H. syriacus-G. raimondii common ancestor 22.28 MYA. Red (H. syriacus) and green (G. raimondii) stars indicate WGD and blue circles indicate diploidization events.
Figure 2 Collinearity block detection and calculation of gene duplication times. (A) Collinearity blocks of the T. cacao genome were detected in G. raimondii and H. syriacus. (B) Calculation of divergence times of individual gene families. Circles and triangles indicate H. syriacus and G. raimondii, respectively, and shade boxes indicate each WGD. (C) Divergence time of Malvales plants. H. syriacus diverged from the H. syriacus-G. raimondii common ancestor 22.28 MYA. Red (H. syriacus) and green (G. raimondii) stars indicate WGD and blue circles indicate diploidization events.CC BY-NC · PubMed Central
Figure 3 Phylogenetic tree of photoperiod/circadian clock genes. (A) The evolutionary history of these genes was inferred using the minimum evolution method. Blue (A. trichopoda), green (A. thaliana), pink (G. raimondii), orange (T. cacao) and red (H. syriacus) indicate genes from each species. (B) Expression patterns of photoperiod/circadian clock genes in petals, ovaries, roots, and leaves.
Figure 3 Phylogenetic tree of photoperiod/circadian clock genes. (A) The evolutionary history of these genes was inferred using the minimum evolution method. Blue (A. trichopoda), green (A. thaliana), pink (G. raimondii), orange (T. cacao) and red (H. syriacus) indicate genes from each species. (B) Expression patterns of photoperiod/circadian clock genes in petals, ovaries, roots, and leaves.CC BY-NC · PubMed Central
Figure 4 Phylogenetic relationships of NBS-LRR genes with >80% bootstrap values. (A) Phylogenetic relationships of predicted NBS-LRR genes in H. syriacus. Red (TNL-A, TNL-B, CNL-5 and RPW-CNL subgroups) indicates expanded subgroups of the H. syriacus genome compared to other plant genomes (Supplementary Table S8). (B) Detailed phylogenetic relationships of expanded TNL subgroups are shown. Intact NB-ARC domains of H. syriacus (red), G. raimondii (green), T. cacao (blue), S. lycopersicum (orange), A. thaliana (light blue) and V. vinifera (purple) were used in the phylogenetic construction.
Figure 4 Phylogenetic relationships of NBS-LRR genes with >80% bootstrap values. (A) Phylogenetic relationships of predicted NBS-LRR genes in H. syriacus. Red (TNL-A, TNL-B, CNL-5 and RPW-CNL subgroups) indicates expanded subgroups of the H. syriacus genome compared to other plant genomes (Supplementary Table S8). (B) Detailed phylogenetic relationships of expanded TNL subgroups are shown. Intact NB-ARC domains of H. syriacus (red), G. raimondii (green), T. cacao (blue), S. lycopersicum (orange), A. thaliana (light blue) and V. vinifera (purple) were used in the phylogenetic construction.CC BY-NC · PubMed Central

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Metadata

Authors
Kim, Y.-M., Kim, S., Koo, N., Shin, A.-Y., Yeom, S.-I., Seo, E., Park, S.-J., Kang, W.-H., Kim, M.-S., Park, J., Jang, I., Kim, P.-G., Byeon, I., Kim, M.-S., Choi, J., Ko, G., Hwang, J., Yang, T.-J., Choi, S.-B., Lee, J. M., Lim, K.-B., Lee, J., Choi, I.-Y., Park, B.-S., Kwon, S.-Y., Choi, D., & Kim, R. W.
Venue
DNA Research
Publisher
Oxford University Press (OUP)
Published
2016-12-22
Pages
dsw049
ISSN
  • 1340-2838
  • 1756-1663
DOI
10.1093/dnares/dsw049
PMC
PMC5381346
Cited by
21
References
2
Language
en

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