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Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

Authors :
Mahmoud Magdy
Lijun Ou
Huiyang Yu
Rong Chen
Yuhong Zhou
Heba Hassan
Bihong Feng
Nathan Taitano
Esther van der Knaap
Xuexiao Zou
Feng Li
Bo Ouyang
Source :
Horticulture Research, Vol 6, Iss 1, Pp 1-15 (2019)
Publication Year :
2019
Publisher :
Oxford University Press, 2019.

Abstract

Abstract Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries among those complexes and identify effective loci for the taxonomical resolution and molecular identification of the studied species/varieties. High-resolution pan-plastomes of five species and two varieties were assembled and compared from 321 accessions. Phyloplastomic and network analyses clarified the taxonomic position of the studied species/varieties and revealed a pronounced number of accessions to be the rare and endemic species, C. galapagoense, that were mistakenly labeled as C. annuum var. glabriusculum among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The rpl23-trnI intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated Capsicum species/varieties. The rps16-trnQ/rbcL-accD/ycf3-trnS gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied Capsicum spp. The pan-plastome approach was shown to be useful in resolving the taxonomical complexes, settling the incomplete lineage sorting conflict and developing a molecular marker set for Capsicum spp. identification.

Details

Language :
English
ISSN :
20527276
Volume :
6
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Horticulture Research
Publication Type :
Academic Journal
Accession number :
edsdoj.915b8b79baa14f2bbf530ad2ebe7bb1a
Document Type :
article
Full Text :
https://doi.org/10.1038/s41438-019-0191-x