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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

ABSTRACT: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

SUBMITTER: Ming R

PROVIDER: S-EPMC2836516 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature

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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Ming Ray R Hou Shaobin S Feng Yun Y Yu Qingyi Q Dionne-Laporte Alexandre A Saw Jimmy H JH Senin Pavel P Wang Wei W Ly Benjamin V BV Lewis Kanako L T KL Salzberg Steven L SL Feng Lu L Jones Meghan R MR Skelton Rachel L RL Murray Jan E JE Chen Cuixia C Qian Wubin W Shen Junguo J Du Peng P Eustice Moriah M Tong Eric E Tang Haibao H Lyons Eric E Paull Robert E RE Michael Todd P TP Wall Kerr K Rice Danny W DW Albert Henrik H Wang Ming-Li ML Zhu Yun J YJ Schatz Michael M Nagarajan Niranjan N Acob Ricelle A RA Guan Peizhu P Blas Andrea A Wai Ching Man CM Ackerman Christine M CM Ren Yan Y Liu Chao C Wang Jianmei J Wang Jianping J Na Jong-Kuk JK Shakirov Eugene V EV Haas Brian B Thimmapuram Jyothi J Nelson David D Wang Xiyin X Bowers John E JE Gschwend Andrea R AR Delcher Arthur L AL Singh Ratnesh R Suzuki Jon Y JY Tripathi Savarni S Neupane Kabi K Wei Hairong H Irikura Beth B Paidi Maya M Jiang Ning N Zhang Wenli W Presting Gernot G Windsor Aaron A Navajas-Pérez Rafael R Torres Manuel J MJ Feltus F Alex FA Porter Brad B Li Yingjun Y Burroughs A Max AM Luo Ming-Cheng MC Liu Lei L Christopher David A DA Mount Stephen M SM Moore Paul H PH Sugimura Tak T Jiang Jiming J Schuler Mary A MA Friedman Vikki V Mitchell-Olds Thomas T Shippen Dorothy E DE dePamphilis Claude W CW Palmer Jeffrey D JD Freeling Michael M Paterson Andrew H AH Gonsalves Dennis D Wang Lei L Alam Maqsudul M

Nature 20080401 7190

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiospe ...[more]

PMID: 18432245

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Project description:BackgroundPapaya (Carica papaya) is an economically important fruit cultivated in the tropical and subtropical regions of China. However, the rapid softening rate after postharvest leads to a short shelf-life and considerable economic losses. Accordingly, understanding the mechanisms underlying fruit postharvest softening will be a reasonable way to maintain fruit quality and extend its shelf-life.ResultsMitogen-activated protein kinases (MAPKs) are conserved and play essential roles in response to biotic and abiotic stresses. However, the MAPK family remain poorly studied in papaya. Here, a total of nine putative CpMAPK members were identified within papaya genome, and a comprehensive genome-wide characterization of the CpMAPKs was performed, including evolutionary relationships, conserved domains, gene structures, chromosomal locations, cis-regulatory elements and expression profiles in response to phytohormone and antioxidant organic compound treatments during fruit postharvest ripening. Our findings showed that nearly all CpMAPKs harbored the conserved P-loop, C-loop and activation loop domains. Phylogenetic analysis showed that CpMAPK members could be categorized into four groups (A-D), with the members within the same groups displaying high similarity in protein domains and intron-exon organizations. Moreover, a number of cis-acting elements related to hormone signaling, circadian rhythm, or low-temperature stresses were identified in the promoters of CpMAPKs. Notably, gene expression profiles demonstrated that CpMAPKs exhibited various responses to 2-chloroethylphosphonic acid (ethephon), 1-methylcyclopropene (1-MCP) and the combined ascorbic acid (AsA) and chitosan (CTS) treatments during papaya postharvest ripening. Among them, both CpMAPK9 and CpMAPK20 displayed significant induction in papaya flesh by ethephon treatment, and were pronounced inhibition after AsA and CTS treatments at 16 d compared to those of natural ripening control, suggesting that they potentially involve in fruit postharvest ripening through ethylene signaling pathway or modulating cell wall metabolism.ConclusionThis study will provide some valuable insights into future functional characterization of CpMAPKs, and hold great potential for further understanding the molecular mechanisms underlying papaya fruit postharvest ripening.

Dataset Information

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Publications

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

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