Molecular Genetics and Genomics

, Volume 290, Issue 2, pp 661–670 | Cite as

Genome sequence comparison reveals a candidate gene involved in male–hermaphrodite differentiation in papaya (Carica papaya) trees

  • Hiroki Ueno
  • Naoya Urasaki
  • Satoshi Natsume
  • Kentaro Yoshida
  • Kazuhiko Tarora
  • Ayano Shudo
  • Ryohei Terauchi
  • Hideo MatsumuraEmail author
Original Paper


The sex type of papaya (Carica papaya) is determined by the pair of sex chromosomes (XX, female; XY, male; and XYh, hermaphrodite), in which there is a non-recombining genomic region in the Y and Yh chromosomes. This region is presumed to be involved in determination of males and hermaphrodites; it is designated as the male-specific region in the Y chromosome (MSY) and the hermaphrodite-specific region in the Yh chromosome (HSY). Here, we identified the genes determining male and hermaphrodite sex types by comparing MSY and HSY genomic sequences. In the MSY and HSY genomic regions, we identified 14,528 nucleotide substitutions and 965 short indels with a large gap and two highly diverged regions. In the predicted genes expressed in flower buds, we found no nucleotide differences leading to amino acid changes between the MSY and HSY. However, we found an HSY-specific transposon insertion in a gene (SVP like) showing a similarity to the Short Vegetative Phase (SVP) gene. Study of SVP-like transcripts revealed that the MSY allele encoded an intact protein, while the HSY allele encoded a truncated protein. Our findings demonstrated that the SVP-like gene is a candidate gene for male-hermaphrodite determination in papaya.


Carica papaya Sex chromosome Yh chromosome Y chromosome Short Vegetative Phase like 



This work is supported by JSPS (Japan Society for the Promotion of Science) Grant no. 25450004, and the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (PROBRAIN). This work was also supported in part by Grants for Excellent Graduate Schools, MEXT (Ministry of Education, Culture, Sports, Science and Technology), Japan.

Supplementary material

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Supplementary material 1 (XLSX 34 kb)
438_2014_955_MOESM2_ESM.pdf (48 kb)
Supplementary material 2 (PDF 47 kb)
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Supplementary material 3 (PDF 534 kb)
438_2014_955_MOESM4_ESM.pdf (26 kb)
Supplementary material 4 (PDF 26 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Hiroki Ueno
    • 1
  • Naoya Urasaki
    • 2
  • Satoshi Natsume
    • 3
  • Kentaro Yoshida
    • 3
  • Kazuhiko Tarora
    • 2
  • Ayano Shudo
    • 2
  • Ryohei Terauchi
    • 3
  • Hideo Matsumura
    • 4
    Email author
  1. 1.Department of Bioscience and Textile TechnologyShinshu UniversityUedaJapan
  2. 2.Okinawa Prefectural Agricultural Research CenterItomanJapan
  3. 3.Iwate Biotechnology Research CenterKitakamiJapan
  4. 4.Gene Research CenterShinshu UniversityUedaJapan

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