Journal of Plant Research

, Volume 129, Issue 4, pp 727–736 | Cite as

Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations

  • Ayako Izuno
  • Masaomi Hatakeyama
  • Tomoaki Nishiyama
  • Ichiro Tamaki
  • Rie Shimizu-Inatsugi
  • Ryuta Sasaki
  • Kentaro K. Shimizu
  • Yuji Isagi
Regular Paper


Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.


Genome Hawaii Heterozygosity Metrosideros PSMC Wild plants 



We are grateful to Keiko Yamada for her instructions and assistances for the mate pair construction experiments and the Functional Genomics Center Zurich for their technical support with Illumina sequencing. We also thank Kanehiro Kitayama, Yusuke Onoda, Yuki Tsujii and Gaku Amada for their supports on leaf sampling, and Hidetoshi Nagamasu of Kyoto University Herbarium (KYO) for his rapid acceptance of our plant specimen. This study was financially supported by grant-in-aid for JSPS research fellows (13J02516) to AI, Grant-in-Aid for Scientific Research on Innovative Areas, “Genetic Bases for the Evolution of Complex Adaptive Traits” of MEXT Japan (KAKENHI 22128008) to TN, Grant-in-Aid for Scientific Research on Innovative Areas, “Correlative Gene System” of MEXT Japan to KKS, and University Research Priority Program of Evolution in Action of the University of Zurich to KKS and RSI.

Supplementary material

10265_2016_822_MOESM1_ESM.docx (124 kb)
Supplementary material 1 (DOCX 123 kb)
10265_2016_822_MOESM2_ESM.pdf (349 kb)
Supplementary material 2 (PDF 349 kb)


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Copyright information

© The Botanical Society of Japan and Springer Japan 2016

Authors and Affiliations

  • Ayako Izuno
    • 1
  • Masaomi Hatakeyama
    • 2
    • 3
  • Tomoaki Nishiyama
    • 4
  • Ichiro Tamaki
    • 5
  • Rie Shimizu-Inatsugi
    • 2
  • Ryuta Sasaki
    • 6
  • Kentaro K. Shimizu
    • 2
  • Yuji Isagi
    • 1
  1. 1.Graduate School of AgricultureKyoto UniversityKyotoJapan
  2. 2.Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
  3. 3.Functional Genomics Center ZurichZurichSwitzerland
  4. 4.Advanced Science Research CenterKanazawa UniversityKanazawaJapan
  5. 5.Gifu Academy of Forest Science and CultureGifuJapan
  6. 6.Organization of Frontier Science and InnovationKanazawa UniversityKanazawaJapan

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