A chromosome-scale genome of Capsicum pubescens provides insights into candidate terpene-associated gene clusters and pan variation of terpene synthases.

Xu Lu, Yupeng Li, Wanting Wang, Zheng Ye, Lin Li, Huizhen Fu, Muhammad Ahsan Altaf, Shanhan Cheng, Zhiwei Wang

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Article in Planta, 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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Xu Lu *State Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Yupeng Li *State Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Wanting Wang *State Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Zheng YeKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.

Lin LiKey Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.

Huizhen FuState Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Muhammad Ahsan AltafState Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Shanhan ChengState Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China.

Zhiwei WangState Key Laboratory of Tropical Crop Breeding, Sanya Institute of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China. wangzhiwei@hainanu.edu.cn.ORCID http://orcid.org/0000-0003-4895-050X

Funding

National Natural Science Foundation of China 32360096

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Abstract

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conclusionA chromosome-scale genome of Capsicum pubescens and comparative pan-TPS analysis support structural characterization and gene-level prioritization of a chromosome-9 terpene-associated candidate locus in this accession. Capsicum pubescens is one of the five domesticated Capsicum species, mainly cultivated in mid- to high-elevation regions of the Americas. Despite its distinctive morphology and fruit traits, genomic resources for C. pubescens remain less developed than those for the widely cultivated C. annuum. Here, we assembled a chromosome-scale reference genome for accession HNUCP0001, spanning 3.70 Gb with a scaffold N50 of 278.01 Mb. Comparative genomics revealed 679 significantly expanded gene families enriched in sesquiterpenoid and triterpenoid biosynthesis. Genome-wide biosynthetic gene-cluster mining identified multiple terpene-associated candidate loci, which were subsequently prioritized using genome-derived structural criteria and Capsicum pubescens-specific expression evidence. Subsequently, we curated the terpene synthase (TPS) repertoire and, across 16 Capsicum genomes, resolved 36 TPS orthogroups with pronounced presence/absence variation, highlighting dynamic lineage-specific diversification. Together, these analyses establish HNUCP0001 as an accession-specific genomic resource and provide a comparative framework for prioritizing terpene-associated TPS genes and candidate BGCs in Capsicum. These candidate loci, together with accession-level transcriptomic and metabolomic evidence, offer testable hypotheses for future functional studies of specialized terpenoid metabolism in C. pubescens.

Indexed as

Alkyl and Aryl TransferasesCapsicumChromosomes, PlantGenome, PlantMultigene FamilyTerpenesChromosome MappingGene Expression Regulation, PlantGenes, PlantPhylogenyPlant ProteinsAlkyl and Aryl TransferasesPlant ProteinsTerpenesterpene synthaseCapsicum pubescensChromosome-scale genome assemblyComparative genomicsPan variationTerpene synthase

Identifiers

PMID42754670

DOI10.1007/s00425-026-05153-1

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