22 Tea Plant Genomes Show Conserved ARR Subgroups and Shell Orthogroup Variation

Tea plants carry a deeply conserved core of response-regulator genes even as the number and identity of genes within the family vary widely between individual genomes, according to a comparative analysis of 22 chromosome-scale tea plant genomes published in BMC Genomics. The study, released on 29 October 2026 as an open-access research article, examined the broad response-regulator family — collectively termed ARR here, comprising type-A, type-B, type-C, and pseudo-response regulators — across the 22 genomes and integrated family composition with phylogenetic, duplication, local genomic variation, and coding-sequence analyses.

In total, the researchers identified 979 ARR genes, with between 36 and 60 members per genome. All eight ARR subgroups were retained in nearly every genome, indicating that the broad functional architecture of the family is conserved across tea plants. At a finer level, however, individual genomes contained only 36 to 49 of the 105 pangenome orthogroups (OGs). Core and soft-core OGs accounted for 17.1 percent of OGs but 40.1 percent of ARR members, while shell OGs accounted for 50.5 percent of OGs and 56.0 percent of members. Copy gains occurred in 25 OGs and added 41 ARR copies, 34 of which belonged to shell OGs, meaning most newly gained copies fell into the variable shell category.

Duplication histories differed markedly among subgroups. Whole-genome duplicates predominated in the RRA, PRR1, and PRR5 subgroups, whereas proximal and tandem duplicates dominated RRB-III. Transposable-element coverage varied primarily by ARR subgroup and gene region rather than by OG retention class or tea type, suggesting that local genomic context shapes the family’s composition more than the retention status of individual orthogroups.

The analysis also mapped structural variation around ARR loci. The team detected 759 distinct structural variants overlapping 45 reference ARR genes and their neighborhoods, with 52.0 percent of those overlaps located in 10-kilobase flanking regions. Among 5,417 retained orthologous pairs, 86.8 percent had Ka/Ks ratios below 1, a pattern of predominance that persisted after excluding low-Ks pairs, although subgroup contrasts proved sensitive to the Ks threshold used. Public transcriptomes from 12 accessions linked 255 ARR genes to tissue profiles, revealing descriptive organ-associated patterns within the matched subset.

The authors conclude that tea ARR diversity is organized around a conserved deep subgroup structure, whereas most variation is concentrated in shell OG membership, subgroup-specific duplication histories, and local structural contexts. The work addresses a limitation the researchers identify with single-reference gene-family analyses, which cannot resolve how deeply conserved functional groups coexist with intraspecific variation in gene content and copy number. Because the findings derive from comparative genomic analysis of tea plant genomes, with transcriptome patterns described as descriptive within the matched subset, the study characterizes the genomic organization of the ARR family rather than testing functional outcomes.

Subject of Research: Comparative genomics of the ARR response-regulator gene family across 22 tea plant genomes

Article Title: Comparative analysis of 22 tea plant genomes reveals conserved ARR subgroups and orthogroup-level variation

Article References: Han, X., Zhang, B., Hou, Y., Wang, F., Jiang, K., Chen, H., Tian, S., He, W., Yao, X., & Lu, L. (2026). Comparative analysis of 22 tea plant genomes reveals conserved ARR subgroups and orthogroup-level variation. BMC Genomics. https://doi.org/10.1186/s12864-026-13500-5

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13500-5

Keywords: tea plant, genomics, ARR genes, response regulators, pangenome, orthogroups, gene duplication, structural variants, phylogenetics, BMC Genomics, transposable elements, Ka/Ks