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Plant J. 2017 Sep;91(6):1108-1128. doi: 10.1111/tpj.13625. Epub 2017 Aug 3.

The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis.

Qin G1,2, Xu C3, Ming R4,5, Tang H4, Guyot R6, Kramer EM7, Hu Y3, Yi X1,2, Qi Y1,2, Xu X3, Gao Z1,2, Pan H1,2, Jian J3, Tian Y3, Yue Z3, Xu Y1,2.

Author information

1
Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
2
Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, Anhui Province, 230031, China.
3
BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
4
Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
5
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA.
6
Institut de Recherche pour le Développement, Diversité, Adaptation et Développement des Plantes, Montpellier, 34394, France.
7
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.

Abstract

Pomegranate (Punica granatum L.) is a perennial fruit crop grown since ancient times that has been planted worldwide and is known for its functional metabolites, particularly punicalagins. We have sequenced and assembled the pomegranate genome with 328 Mb anchored into nine pseudo-chromosomes and annotated 29 229 gene models. A Myrtales lineage-specific whole-genome duplication event was detected that occurred in the common ancestor before the divergence of pomegranate and Eucalyptus. Repetitive sequences accounted for 46.1% of the assembled genome. We found that the integument development gene INNER NO OUTER (INO) was under positive selection and potentially contributed to the development of the fleshy outer layer of the seed coat, an edible part of pomegranate fruit. The genes encoding the enzymes for synthesis and degradation of lignin, hemicelluloses and cellulose were also differentially expressed between soft- and hard-seeded varieties, reflecting differences in their accumulation in cultivars differing in seed hardness. Candidate genes for punicalagin biosynthesis were identified and their expression patterns indicated that gallic acid synthesis in tissues could follow different biochemical pathways. The genome sequence of pomegranate provides a valuable resource for the dissection of many biological and biochemical traits and also provides important insights for the acceleration of breeding. Elucidation of the biochemical pathway(s) involved in punicalagin biosynthesis could assist breeding efforts to increase production of this bioactive compound.

KEYWORDS:

adaption; genome; pomegranate; punicalagin biosynthesis; system evolution

PMID:
28654223
DOI:
10.1111/tpj.13625
[Indexed for MEDLINE]
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