Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron

doi:10.1016/j.pld.2025.04.006

Plant Diversity ›› 2025, Vol. 47 ›› Issue (04): 593-603.DOI: 10.1016/j.pld.2025.04.006

Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron

Zhi-Qiong Mo (莫智琼)^a,b,c, Chao-Nan Fu (付超男)^b,d, Alex D. Twyford^e,f, Pete M. Hollingsworth^f, Ting Zhang (张挺)^b, Jun-Bo Yang (杨俊波)^b, De-Zhu Li (李德铢)^b,d,g, Lian-Ming Gao (高连明)^a,d,g

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omits, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
e. Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, Scotland, UK;
f. Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK;
g. Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China

收稿日期:2025-02-25 修回日期:2025-04-17 出版日期:2025-08-13 发布日期:2025-08-13
通讯作者: Lian-Ming Gao (高连明),E-mail:gaolm@mail.kib.ac.cn
基金资助:
This study was supported by the National Key Research and Development Program of China (2023YFA0915800), the Science and Technology Basic Resources Investigation Program (2021FY100200), the Key Basic Research program of Yunnan Province, China (202101BC070003), the Large-scale Scientific Facilities of the Chinese Academy of Sciences (2017-LSFGBOWS-02), and the Chinese Academy of Sciences President's International Fellowship Initiative (2025PD0021). We are grateful to curator of KUN to access the herbarium specimens, and Jiayun Zou, Zhirong Zhang, Jing Yang, Hongtao Li and Chunxia Zeng, for their help with sample collection, laboratory work and data analysis. Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High-Performance Computing Center of Germplasm Bank of Wild Species, Kunming Institute of Botany, CAS.

Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omits, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
e. Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, Scotland, UK;
f. Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK;
g. Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China

Received:2025-02-25 Revised:2025-04-17 Online:2025-08-13 Published:2025-08-13
Contact: Lian-Ming Gao (高连明),E-mail:gaolm@mail.kib.ac.cn
Supported by:
This study was supported by the National Key Research and Development Program of China (2023YFA0915800), the Science and Technology Basic Resources Investigation Program (2021FY100200), the Key Basic Research program of Yunnan Province, China (202101BC070003), the Large-scale Scientific Facilities of the Chinese Academy of Sciences (2017-LSFGBOWS-02), and the Chinese Academy of Sciences President's International Fellowship Initiative (2025PD0021). We are grateful to curator of KUN to access the herbarium specimens, and Jiayun Zou, Zhirong Zhang, Jing Yang, Hongtao Li and Chunxia Zeng, for their help with sample collection, laboratory work and data analysis. Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High-Performance Computing Center of Germplasm Bank of Wild Species, Kunming Institute of Botany, CAS.

摘要/Abstract

摘要： Deep genome skimming (DGS) has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses. However, its reliability with low DNA quality and quantity typical of archival specimens, such as herbarium material, remains largely unexplored. We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales. We first investigated locus recovery variation with sequencing depth, before evaluating the phylogenetic utility of different sets of loci, including Angiosperms353, target nuclear exons, and extended exon-flanking regions. We found DGS effectively recovered nuclear genes from herbarium specimens, with ～15×coverage performing similarly to deeper sequencing. The recovery of target exon and flanking regions was improved by using supercontigs as a reference, offering a potential solution to limited sequencing depth. The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron. Notably, exon-flanking regions showed significant potential for resolving relationships at shallow scales. Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees. This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies, and makes recommendations for best practices regarding sequencing coverage, locus selection, and bioinformatic approaches.

关键词: Herbarium specimens, Degraded DNA, Deep genome skimming, Target enrichment, Non-targeted exon-flanking regions, Phylogenomics

Abstract: Deep genome skimming (DGS) has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses. However, its reliability with low DNA quality and quantity typical of archival specimens, such as herbarium material, remains largely unexplored. We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales. We first investigated locus recovery variation with sequencing depth, before evaluating the phylogenetic utility of different sets of loci, including Angiosperms353, target nuclear exons, and extended exon-flanking regions. We found DGS effectively recovered nuclear genes from herbarium specimens, with ～15×coverage performing similarly to deeper sequencing. The recovery of target exon and flanking regions was improved by using supercontigs as a reference, offering a potential solution to limited sequencing depth. The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron. Notably, exon-flanking regions showed significant potential for resolving relationships at shallow scales. Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees. This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies, and makes recommendations for best practices regarding sequencing coverage, locus selection, and bioinformatic approaches.

Key words: Herbarium specimens, Degraded DNA, Deep genome skimming, Target enrichment, Non-targeted exon-flanking regions, Phylogenomics

Zhi-Qiong Mo (莫智琼), Chao-Nan Fu (付超男), Alex D. Twyford, Pete M. Hollingsworth, Ting Zhang (张挺), Jun-Bo Yang (杨俊波), De-Zhu Li (李德铢), Lian-Ming Gao (高连明). Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron[J]. Plant Diversity, 2025, 47(04): 593-603.

参考文献

Aguirre-Santoro, J., Zuluaga, A., Stonesmyth, E., et al., 2024. Phylogenomics of Puya (Bromeliaceae):evolution in the Andean slopes and sky island ecosystems. J. Syst. Evol. 62, 257-274.
Bakker, F.T., Lei, D., Yu, J., et al., 2016. Herbarium genomics:plastome sequence assembly from a range of herbarium specimens using an iterative organelle genome assembly pipeline. Biol. J. Linn. Soc. 117, 33-43.
Bankevich, A., Nurk, S., Antipov, D., et al., 2012. SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477.
Borowiec, M.L., 2016. AMAS:a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4, e1660.
Burbano, H.A., Gutaker, R.M., 2023. Ancient DNA genomics and the renaissance of herbaria. Science 382, 59-63.
Capella-Gutierrez, S., Silla-Martinez, J.M., Gabaldon, T., 2009. trimAl:a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973.
Chamberlain, D., Hyam, R., Argent, G., et al., 1996. The genus Rhododendron:its classification and synonymy. Oxford:The Alden Press.
Chang, Y., Zhang, R., Ma, Y., et al., 2023. A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data. Sci. Data 10, 451.
Chen, S., Zhou, Y., Chen, Y., et al., 2018. fastp:an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, 884-890.
Chen, Y.P., Sunojkumar, P., Spicer, R.A., et al., 2025. Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes. Mol. Biol. Evol. 42, msaf011.
Diaz-Garcia, L., Garcia-Ortega, L.F., Gonzalez-Rodriguez, M., et al., 2021. Chromosome-level genome assembly of the American cranberry (Vaccinium macrocarpon Ait.) and its wild relative Vaccinium microcarpum. Front. Plant Sci. 12, 633310.
Dodsworth, S., Pokorny, L., Johnson, M.G., et al., 2019. Hyb-Seq for flowering plant systematics. Trends Plant Sci. 24, 887-891.
Emms, D.M., Kelly, S., 2015. OrthoFinder:solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157.
Freyman, W.A., Johnson, M.G., Rothfels, C.J., 2023. homologizer:phylogenetic phasing of gene copies into polyploid subgenomes. Methods Ecol. Evol. 14, 1230-1244.
Fu, C.N., Mo, Z.Q., Yang, J.B., et al., 2022. Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron. Mol. Ecol. Resour. 22, 404-414.
Guo, C., Luo, Y., Gao, L.M., et al., 2023. Phylogenomics and the flowering plant tree of life. J. Integr. Plant Biol. 65, 299-323.
Hoang, D.T., Chernomor, O., von Haeseler, A., et al., 2018. UFBoot2:improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518-522.
Jin, Z.T., Hodel, R.G.J., Ma, D.K., et al., 2023. Nightmare or delight:taxonomic circumscription meets reticulate evolution in the phylogenomic era. Mol. Phylogenet. Evol. 189, 107914.
Jin, Z.T., Ma, D.K., Liu, G.N., et al., 2024. Advancing Pyrus phylogeny:deep genome skimming-based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae). Taxon 73, 784-799.
Johnson, M.G., Gardner, E.M., Liu, Y., et al., 2016. Hybpiper:extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant Sci. 4, 1600016.
Johnson, M.G., Pokorny, L., Dodsworth, S., et al., 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Syst. Biol. 68, 594-606.
Junier, T., Zdobnov, E.M., 2010. The Newick utilities:high-throughput phylogenetic tree processing in the Unix shell. Bioinformatics 26, 1669-1670.
Kadlec, M., Bellstedt, D.U., Le Maitre, N.C., et al., 2017. Targeted NGS for species level phylogenomics:"made to measure" or "one size fits all"? PeerJ 5, e3569.
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., et al., 2017. ModelFinder:fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587-589.
Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Mol. Biol. Evol. 30, 772-780.
Kent, W.J., 2002. BLAT-The BLAST-like alignment tool. Genome Res. 12, 656-664.
Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
Lemmon, E.M., Lemmon, A.R., 2013. High-throughput genomic data in systematics and phylogenetics. Annu. Rev. Ecol. Evol. Syst. 44, 99-121.
Li, H., Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
Li, W., Godzik, A., 2006. Cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659.
Liu, B.B., Hong, D.Y., Zhou, S.L., et al., 2019. Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae). J. Syst. Evol. 57, 678-694.
Liu, B.B., Liu, G.N., Hong, D.Y., Wen, J., 2020. Eriobotrya belongs to Rhaphiolepis (Maleae, Rosaceae):evidence from chloroplast genome and nuclear ribosomal DNA data. Front. Plant Sci. 10, 1731.
Liu, B.B., Ma, Z.Y., Ren, C., et al., 2021. Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics:a case study in Vitaceae. J. Syst. Evol. 59, 1124-1138.
Liu, B.B., Ren, C., Kwak, M., et al., 2022. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. J. Integr. Plant Biol. 64, 1020-1043.
Ma, H., Liu, Y.B., Liu, D.T., et al., 2021. Chromosome-level genome assembly and population genetic analysis of a critically endangered Rhododendron provide insights into its conservation. Plant J. 107, 1533-1545.
Ma, Y.Z., Mao, X.X., Wang, J., et al., 2022. Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China. Natl. Sci. Rev. 9, nwac276.
Maurin, O., Anest, A., Bellot, S., et al., 2021. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. Am. J. Bot. 108, 1087-1111.
Mo, Z.Q., Fu, C.N., Zhu, M.S., et al., 2022. Resolution, conflict and rate shifts:insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae). Ann. Bot. 130, 687-701.
Nauheimer L., Weigner N., Joyce E., et al., 2021. HybPhaser:a workflow for the detection and phasing of hybrids in target capture datasets. Appl. Plant Sci. 9, e11441.
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., et al., 2015. IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268-274.
Ning, W., Meudt, H.M., Tate, J.A., 2024. A roadmap of phylogenomic methods for studying polyploid plant genera. Appl. Plant Sci. 12, e11580.
Shirasawa, K., Kobayashi, N., Nakatsuka, A., et al., 2021. Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense. DNA Res. 28, dsab010.
Simmons, M.P., Maurin, O., Bailey, P., et al., 2022. Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics 38, 595-611.
Slater, G.S., Birney, E., 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31.
Smith, S.A., Moore, M.J., Brown, J.W., et al., 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150.
Soza, V.L., Lindsley, D., Waalkes, A., et al., 2019. The Rhododendron genome and chromosomal organization provide insight into shared whole-genome duplications across the heath family (Ericaceae). Genome Biol. Evol. 11, 3353-3371.
Staats, M., Erkens, R.H.J., van de Vossenberg, B., et al., 2013. Genomic treasure troves:complete genome sequencing of herbarium and insect museum specimens. PLoS One 8, e69189.
Stamatakis, A., 2014. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313.
Su, N., Hodel, R., Wang, X., et al., 2023. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. Plant Divers. 45, 397-408.
Vargas, O.M., Heuertz, M., Smith, S.A., et al., 2019. Target sequence capture in the Brazil nut family (Lecythidaceae):marker selection and in silico capture from genome skimming data. Mol. Phylogenet. Evol. 135, 98-104.
Villaverde, T., Pokorny, L., Olsson, S., et al., 2018. Bridging the micro-and macroevolutionary levels in phylogenomics:Hyb-Seq solves relationships from populations to species and above. New Phytol. 220, 636-650.
Wang, J., Luo, J., Ma, Y.Z., et al., 2019. Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain. J. Syst. Evol. 57, 278-286.
Wang, X.Q., Xiong, T., Wang, Y.Y., et al., 2024. Integrating genomic sequencing resources:an innovative perspective on recycling with universal Angiosperms353 probe sets. Hortic. Adv. 2, 4.
Wang, X.Y., Gao, Y., Wu, X.P., et al., 2021. High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution. Plant Biotechnol. J. 19, 2544-2560.
Weitemier, K., Straub, S.C.K., Cronn, R.C., et al., 2014. Hyb-Seq:combining target enrichment and genome skimming for plant phylogenomics. Appl. Plant Sci. 2, 1400042.
Xia, X.M., Du, H.L., Hu, X.D., et al., 2024. Genomic insights into adaptive evolution of the species-rich cosmopolitan plant genus Rhododendron. Cell Reports 43, 114745.
Xia, X.M., Yang, M.Q., Li, C.L., et al., 2022. Spatiotemporal evolution of the global species diversity of Rhododendron. Mol. Biol. Evol. 39, msab314.
Xue, T.T., Janssens, S.B., Liu, B.B., et al., 2023. Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories:a case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae). Mol. Phylogenet. Evol. 190, 107956.
Yang, F.S., Nie, S., Liu, H., et al., 2020. Chromosome-level genome assembly of a parent species of widely cultivated azaleas. Nat. Commun. 11, 5269.
Yang, L.H., Shi, X.Z., Wen, F., et al., 2023. Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae). Ann. Bot. 131, 953-966.
Yang, Y., Smith, S.A., 2014. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes:improving accuracy and matrix occupancy for phylogenomics. Mol. Biol. Evol. 31, 3081-3092.
Yardeni, G., Viruel, J., Paris, M., et al., 2022. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol. Ecol. Resour. 22, 927-945.
Yu, J.R., Zhao, H., Niu, Y.T., et al., 2023. Distinct hybridization modes in wide-and narrow-ranged lineages of Causonis (Vitaceae). BMC Biology 21, 209.
Yu, X.Q., Yang, D., Guo, C., et al., 2018. Plant phylogenomics based on genome-partitioning strategies:progress and prospects. Plant Divers. 40, 158-164.
Zeng, C.X., Hollingsworth, P.M., Yang, J., et al., 2018. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods 14, 43.
Zhang, C., Rabiee, M., Sayyari, E., et al., 2018. ASTRAL-III:polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19, 153.
Zhang, C., Zhao, Y., Braun, E.L., et al., 2021. TAPER:pinpointing errors in multiple sequence alignments despite varying rates of evolution. Methods Ecol. Evol. 12, 2145-2158.
Zhang, F., Ding, Y.H., Zhu, C.D., et al., 2019. Phylogenomics from low-coverage whole-genome sequencing. Methods Ecol. Evol. 10, 507-517.
Zhang, G.J., Ma, H., 2024. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. J. Integr. Plant Biol. 66, 546-578.
Zhang, L., Xu, P., Cai, Y., et al., 2017. The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. GigaScience 6, gix076.
Zuntini, A.R., Carruthers, T., Maurin, O., et al., 2024. Phylogenomics and the rise of the angiosperms. Nature 629, 843-850.

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Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron

Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus Rhododendron

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