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

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成果类型:
期刊论文
作者:
Magdy, Mahmoud;Ou, Lijun;Yu, Huiyang;Chen, Rong;Zhou, Yuhong;Hassan, Heba;Feng, Bihong;Taitano, Nathan;van der Knaap, Esther;Zou, Xuexiao;Li, Feng;Ouyang, Bo*
通讯作者:
Ouyang, Bo
作者机构:
[Chen, Rong; Zhou, Yuhong; Magdy, Mahmoud; Hassan, Heba; Li, Feng; Ouyang, Bo; Yu, Huiyang] Huazhong Agr Univ, Minist Educ, Key Lab Hort Plant Biol, Wuhan 430070, Hubei, Peoples R China.
[Magdy, Mahmoud] Ain Shams Univ, Fac Agr, Genet Dept, Cairo 11241, Egypt.
[Ou, Lijun; Zou, Xuexiao] Hunan Agr Univ, Coll Hort & Landscape, Changsha 410128, Hunan, Peoples R China.
[Feng, Bihong] Guangxi Univ, Coll Agr, Nanning 530004, Peoples R China.
[van der Knaap, Esther; Taitano, Nathan] Univ Georgia, Coll Agr & Environm Sci, Dept Hort, Athens, GA 30602 USA.
通讯机构:
[Ouyang, Bo] Huazhong Agr Univ, Minist Educ, Key Lab Hort Plant Biol, Wuhan 430070, Hubei, Peoples R China.
语种:
英文
关键词:
Agricultural genetics;Comparative genomics;Genetic markers;Phylogenomics
期刊:
Horticulture research
ISSN:
2052-7276
年:
2019
卷:
6
页码:
108
文献类别:
WOS:Article
所属学科:
ESI学科类别:农业科学;WOS学科类别:Horticulture;Plant Sciences
入藏号:
基金类别:
National Key Research and Development Program of China [2016YFD0101704]; Fundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities [2662017PY036]; China Post-Doc Organization (Post-Doctoral grant) [192704]
机构署名:
本校为其他机构
院系归属:
园艺园林学院
摘要:
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-trnl 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.
参考文献:
Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI 10.1073/pnas.0812297106
Benson G, 1999, NUCLEIC ACIDS RES, V27, P573, DOI 10.1093/nar/27.2.573
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