Evidence map›Paper›PMID 42841991›Full record

ArticlePlant cell reports2026

Comparative analysis of plastomes of Rubus cultivars and development of molecular markers for species delimitation.

Lichao Hu, Yaqiong Wu, Zhuang Zhao, Wenlong Wu, Fuliang Cao, Zefu Wang, Weilin Li

Abstract readComparative Study
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In one paragraph

Article in Plant cell reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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7 authors.

Lichao Hu *State Key Laboratory of Development and Utilization of Forest Food Resources, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, College of Soil and Water Conservation, Nanjing Forestry University, Nanjing, 210037, China.
Yaqiong Wu *Jiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
Zhuang ZhaoState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China.
Wenlong WuJiangsu Provincial Key Laboratory for Plant Taxonomy, Resource Conservation and Utilization, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China.
Fuliang CaoState Key Laboratory of Development and Utilization of Forest Food Resources, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, College of Soil and Water Conservation, Nanjing Forestry University, Nanjing, 210037, China.
Zefu WangState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China. wangzefu@njfu.edu.cn.
Weilin LiState Key Laboratory of Development and Utilization of Forest Food Resources, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, College of Soil and Water Conservation, Nanjing Forestry University, Nanjing, 210037, China. wlli@njfu.edu.cn.

Funding

the China Postdoctoral Science Foundation 2025M781855the "JBGS" Project of Seed Industry Revitalization in Jiangsu Province JBGS [2021] 021the State Key Laboratory for Development and Utilization of Forest Food Resources No. SLFF-KF2026-09
6 · The paper itself

Abstract

key messagePlastome analyses confirmed the taxonomic classification of cultivated Rubus and identified candidate InDel markers for distinguishing major cultivated groups, offering genetic resources for future studies of hybrid identification and breeding. The genus Rubus, belonging to the Rosaceae family, comprises numerous wild germplasm resources. Among its most economically valuable cultivars are red raspberry, black raspberry, blackberry, as well as raspberry × blackberry hybrids. In this study, we assembled and characterized 81 newly Rubus plastomes, including 22 wild species and 59 cultivars. All genomes exhibited the typical quadripartite structure, with sizes ranging from 155,385 to 157,012 bp and containing 130 annotated genes (113 unique functional genes), indicating a high degree of conservation in plastome architecture and gene order. A comparative analysis was further conducted using plastomes from 16 representative Rubus cultivars, representing all unique plastome sequences. The repeat sequences, codon usage bias, and hypervariable regions were systematically analyzed. Phylogenetic analysis revealed that modern Rubus cultivars primarily cluster within three subgenera: Rubus, Idaeobatus, and Melanobatus, with black raspberry phylogenetically placed within Melanobatus. Furthermore, four InDel markers were developed and validated for distinguishing three Rubus cultivar groups (black raspberry, red raspberry and hybrids). In summary, our research substantially expands available plastome resources for Rubus species and cultivars, thereby facilitating species delimitation and supporting future hybrid breeding.

Indexed as

Genome, PlastidRubusGenetic MarkersGenome, PlantINDEL MutationPhylogenySpecies SpecificityGenetic MarkersMolecular markerPhylogenetic analysisRubus, plastomeSpecies delimitation

Identifiers

PMID42841991

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