Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae)

Abstract

How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBF s, ERF-VII s, and RAD51C ) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNL s, prRLP s, and XII RLK s), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3 ) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.

Acknowledgements

This work was supported by grants from the Science Fund for Creative Research Groups of the National Natural Science Foundation of China (No. 32221001), the National Natural Science Foundation of China (General Program) (No. 32070233), the National Key Research Development Program of China (No. 2023YFF0805800), and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (No. 72202200205). We thank Rong-Hua Liang and Jin-Dan Zhang from the Plant Science Facility of the Institute of Botany, Chinese Academy of Sciences, for their excellent technical assistance. We thank Li-Xin Zhou for providing plant photo.

Author contributions

Z.D.C. and D.E.S. led and managed the project; Z.D.C. and J.Z. conceived the study; J.Z., K.L.D., and M.Z.R. wrote the manuscript; Z.D.C., J.F.Y., and B.L. collected and identified the plant materials, and provided the photos of the investigated plants; X.X.F., G.Z., J.Z., K.L.D., M.Z.R., and Y.T.N. cultured and prepared materials; X.X.F. and J.Z. performed the flow cytometry estimate; X.X.F., J.Z., and D.M.Z. performed the chromosome number estimate; Z.W.W. and X.Z. assembled and annotated the genomes and transcriptomes; Z.W.W., X.Z., and J.Z. performed phylogenomic and divergence time analyses; K.L.D., M.Z.R., and J.Z. analyzed gene families; Z.W.W., X.Z., and J.Z. conducted WGD analysis; Z.W.W., X.Z., W.J.S., and M.Z.W. performed gene expression and functional enrichment analyses; Z.W.W., X.Z., J.Z., and K.L.D. detected the FEGs and PSGs. Z.D.C., D.E.S., P.S.S., Z.J.L., J.H.L., L.M.L., and J.X.S. evaluated the results and contributed substantially to revisions. All authors read and approved the manuscript.

Data availability

The raw sequencing data of the T. glandulifera genome and transcriptome have been deposited in the National Genomics Data Center (https://ngdc.cncb.ac.cn/, CNCB) under the BioProject accession number PRJCA019252. The T. glandulifera genome assembly and annotation files have been submitted to FigShare (http://doi.org/10.6084/m9.figshare.25018103). The RNA-seq reads of 13 Dipsacales species are available from CNCB under the BioProject accession number PRJCA019358. Public transcriptomes used in this study are available from NCBI under the accession numbers SRX7804715 and DRX054302. All data are available from the corresponding author upon reasonable request.

Conflict of interest statement

The authors declare no competing interests.

Supplementary data

Supplementary data are available at Horticulture Research online.

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