Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

Shen, Weixiang; Dong, Zhanghong; Zhao, Wenzhi; Ma, Luyao; Wang, Fei; Li, Weiying; Xin, Peiyao

doi:10.3390/horticulturae8090788

Open AccessArticle

Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

by

Weixiang Shen

^1,2

,

Zhanghong Dong

^1,2

,

Wenzhi Zhao

^1,2,

Luyao Ma

^1,2,

Fei Wang

^1,2,

Weiying Li

^1,2 and

Peiyao Xin

^1,2,*

¹

Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China

²

Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China

^*

Author to whom correspondence should be addressed.

Horticulturae 2022, 8(9), 788; https://doi.org/10.3390/horticulturae8090788

Submission received: 23 June 2022 / Revised: 10 August 2022 / Accepted: 26 August 2022 / Published: 30 August 2022

(This article belongs to the Special Issue Genetic Improvement of Horticultural Plants with Special Emphasis on Ornamentals)

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Abstract

Rosa lucieae is one of the famous wild ancestors of cultivated roses and plays a very important role in horticultural research, but there is still a lack of research on the R. lucieae chloroplast genome. In this study, we used the Illumina MiSeq platform for sequencing, assembly, and annotation to obtain the R. lucieae chloroplast genome sequencing information and compared genomics, selection stress analysis, and phylogenetic analysis with 12 other chloroplast genomes of Rosa. The R. lucieae cpDNA sequence has a total length of 156,504 bp, and 130 genes are annotated. The length of all 13 studied chloroplast genomes is 156,333~157,385 bp. Their gene content, gene sequence, GC content, and IR boundary structure were highly similar. Five kinds of large repeats were detected that numbered 100~116, and SSR sequences ranged from 78 to 90 bp. Four highly differentiated regions were identified, which can be used as potential genetic markers for Rosa. Selection stress analysis showed that there was significant positive selection among the 18 genes. The phylogenetic analysis of R. lucieae and R. cymose, R. maximowicziana, R. multiflora, and R. pricei showed the closest relationship. Overall, our results provide a more comprehensive understanding of the systematic genomics and comparative genomics of Rosa.

Keywords: Rosa; plastid; repeat sequence; positive selection; phylogenetic analysis

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MDPI and ACS Style

Shen, W.; Dong, Z.; Zhao, W.; Ma, L.; Wang, F.; Li, W.; Xin, P. Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics. Horticulturae 2022, 8, 788. https://doi.org/10.3390/horticulturae8090788

AMA Style

Shen W, Dong Z, Zhao W, Ma L, Wang F, Li W, Xin P. Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics. Horticulturae. 2022; 8(9):788. https://doi.org/10.3390/horticulturae8090788

Chicago/Turabian Style

Shen, Weixiang, Zhanghong Dong, Wenzhi Zhao, Luyao Ma, Fei Wang, Weiying Li, and Peiyao Xin. 2022. "Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics" Horticulturae 8, no. 9: 788. https://doi.org/10.3390/horticulturae8090788

APA Style

Shen, W., Dong, Z., Zhao, W., Ma, L., Wang, F., Li, W., & Xin, P. (2022). Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics. Horticulturae, 8(9), 788. https://doi.org/10.3390/horticulturae8090788

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Complete Chloroplast Genome Sequence of Rosa lucieae and Its Characteristics

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