Tropical Plant Biology

, Volume 1, Issue 3–4, pp 246–277 | Cite as

Fruit Development, Ripening and Quality Related Genes in the Papaya Genome

  • Robert E. PaullEmail author
  • Beth Irikura
  • Pingfang Wu
  • Helen Turano
  • Nancy Jung Chen
  • Andrea Blas
  • John K. Fellman
  • Andrea R. Gschwend
  • Ching Man Wai
  • Qingyi Yu
  • Gernot Presting
  • Maqsudul Alam
  • Ray Ming


Papaya (Carica papaya L.) is the first fleshy fruit with a climacteric ripening pattern to be sequenced. As a member of the Rosids superorder in the order Brassicales, papaya apparently lacks the genome duplication that occurred twice in Arabidopsis. The predicted papaya genes that are homologous to those potentially involved in fruit growth, development, and ripening were investigated. Genes homologous to those involved in tomato fruit size and shape were found. Fewer predicted papaya expansin genes were found and no Expansin Like-B genes were predicted. Compared to Arabidopsis and tomato, fewer genes that may impact sugar accumulation in papaya, ethylene synthesis and response, respiration, chlorophyll degradation and carotenoid synthesis were predicted. Similar or fewer genes were found in papaya for the enzymes leading to volatile production than so far determined for tomato. The presence of fewer papaya genes in most fruit development and ripening categories suggests less subfunctionalization of gene action. The lack of whole genome duplication and reductions in most gene families and biosynthetic pathways make papaya a valuable and unique tool to study the evolution of fruit ripening and the complex regulatory networks active in fruit ripening.


Fruit growth Expansins Ethylene Respiration Carotenoids Chlorophyll Volatiles Sugar accumulation 

Supplementary material

12042_2008_9021_MOESM1_ESM.doc (49 kb)
Supplementary Table 1 List of predicted papaya expansins genes, the whole genome shotgun sequence accession number in NCBI (WGS Accession), coding sequence for amino acids (CDS), the number of introns in the nucleotide sequence (introns), amino acids (aa), whether a secretory sequence was predicted (secretory) its location (ER endoplasmic retriculum), presence of discrete portion of protein possessing its own function and the superfamily (domain), similarity in peptide sequence with another species (homology), E-value was the expectation value for homology, and the number of papaya expressed sequence tags (EST) detected of at least 500 bases and 99% identity. (DOC 49 KB)
12042_2008_9021_MOESM2_ESM.doc (54 kb)
Supplementary Table 2 Predicted papaya ethylene response factors (ERF), the whole genome shotgun sequence accession number in NCBI (WGS Accession), coding sequence for amino acids (CDS), the number of introns in the nucleotide sequence (introns), amino acids (aa), presence of discrete portion of protein possessing its own function and the superfamily (domain), similarity in peptide sequence with another species (homology), extent the sequences were invariant (identity), E-value was the expectation value for homology, and the number of papaya expressed sequence tags (EST) detected of at least 500 bases and 99% identity. (DOC 54.5 KB)
12042_2008_9021_MOESM3_ESM.doc (24 kb)
Supplementary Table 3 Latex associated genes, the whole genome shotgun sequence accession number in NCBI (WGS Accession), coding sequence for amino acids (CDS), amino acids (aa), whether a secretory sequence was predicted (secretory) its location (mito mitchondria), presence of discrete portion of protein possessing its own function and the superfamily (domain), similarity in peptide sequence with another species (homology), extent the sequences were invariant (identity), E-value was the expectation value for homology, and the number of papaya expressed sequence tags (EST) detected of at least 500 bases and 99% identity. (DOC 24 KB)
12042_2008_9021_MOESM4_ESM.doc (54 kb)
Supplementary Table 4 Predicted papaya genes for lignin biosynthesis, the whole genome shotgun sequence accession number in NCBI (WGS Accession), coding sequence for amino acids (CDS), the number of introns in the nucleotide sequence (introns), amino acids (aa), presence of discrete portion of protein possessing its own function and the superfamily (domain), similarity in peptide sequence with another species (homology), extent the sequences were invariant (identity), E-value was the expectation value for homology, and the number of papaya expressed sequence tags (EST) detected of at least 500 bases and 99% identity. (DOC 54 KB)
12042_2008_9021_MOESM5_ESM.doc (66 kb)
Supplementary Table 5 Predicted peroxidases (Peroxidase Superfamily) genes in the papaya genome, the whole genome shotgun sequence accession number in NCBI (WGS Accession), coding sequence for amino acids (CDS), amino acids (aa), similarity in peptide sequence with another species (homology), extent the sequences were invariant (identity), E-value was the expectation value for homology, and the number of papaya expressed sequence tags (EST) detected of at least 500 bases and 99% identity. (DOC 66.5 KB)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Robert E. Paull
    • 1
    Email author
  • Beth Irikura
    • 1
  • Pingfang Wu
    • 1
  • Helen Turano
    • 1
  • Nancy Jung Chen
    • 1
  • Andrea Blas
    • 2
  • John K. Fellman
    • 3
  • Andrea R. Gschwend
    • 4
  • Ching Man Wai
    • 1
  • Qingyi Yu
    • 5
  • Gernot Presting
    • 2
  • Maqsudul Alam
    • 6
  • Ray Ming
    • 4
  1. 1.Department of Tropical Plant and Soil SciencesUniversity of Hawaii at ManoaHonoluluUSA
  2. 2.Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluUSA
  3. 3.Department of Horticulture and Landscape ArchitectureWashington State UniversityPullmanUSA
  4. 4.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  5. 5.Hawaii Agriculture Research CenterAieaUSA
  6. 6.Advanced Studies in Genomics, Proteomics and BioinformaticsUniversity of HawaiiHonoluluUSA

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