Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes

Li, Yunxia; Zhang-hai, LI; Schuiteman, André; Chase, Mark W.; Li, Jianwu; Huang, Wei-Chang; Hidayat, Arief; Wu, Shasha; Jin, Xiao‐Hua

doi:10.1016/j.ympev.2019.106540

Cited by 85 publications

(123 citation statements)

References 77 publications

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“…1, inset). Unsupported relationships were restricted to Epidendroideae and Arundina+remainder of Arethuseae 27 , and the position of Eulophiinae in the Cymbidieae 25,28,49 ( Fig. 2).…”

Section: Phylogenetic Relationships and Divergence Times In The Orchimentioning

confidence: 99%

“…Previous orchid studies have failed to resolve relationships in rapidly diversifying clades [24][25][26] because of reduced taxon and data sampling 27 . This is particularly true for Cymbidieae and Pleurothallidinae, the two most species-rich groups in which generic relationships are largely the product of rapid diversification 28 that is difficult to resolve using only a few loci 25,29 .…”

Section: Introductionmentioning

confidence: 99%

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Serna-Sánchez

Pérez‐Escobar

Bogarín

et al. 2019

Preprint

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24 Recent phylogenomic analyses have solved evolutionary relationships between most of the 25 Orchidaceae subfamilies and tribes, yet phylogenetic relationships remain unclear within the 26 42 43 45 46 47 100, PP = 0.77-1.0), and only a few positions remained unresolved. Here, the relationship between 128 Codonorchidae+Orchideae was moderately supported (LBS = 86) together with that of 129 Cymbidiinae and the remaining Cymbidieae (LBS = 62). The monophyly of Nervilieae and 130 Triphoreae was moderately supported (LBS = 79), as well as the phylogenetic relationships of 131 Nervilieae+Triphoreae and the remainder of Epidendroideae (LBS = 75), and Epidendreae and 132 Coelia + Eria (LBS = 52) (Fig. 2). 133 134 2.3 Molecular characterisation of plastid genomes 135 Whole plastome sequences belonging to 97 species (11 sequenced here and 86 reported in 136 NCBI) were annotated for 75 protein-coding genes. Five additional genes were recovered when 137 concatenating this data matrix with the protein coding regions matrix used by Givnish 2 , giving a 138 6

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“…1, inset). Unsupported relationships were restricted to Epidendroideae and Arundina+remainder of Arethuseae 27 , and the position of Eulophiinae in the Cymbidieae 25,28,49 ( Fig. 2).…”

Section: Phylogenetic Relationships and Divergence Times In The Orchimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Serna-Sánchez

Pérez‐Escobar

Bogarín

et al. 2019

Preprint

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“…Some differences among these techniques include 1) how capture probes are designed, e.g., whether they target dozens (de Sousa et al, 2014) to thousands (Mandel et al, 2014;Weitemier et al, 2014) of more or less conserved genomic regions; 2) if the focus is taxon-specific (e.g., Gossypium, Grover et al, 2015;Sabal, Heyduk et al, 2016;Helianthus, Stephens et al, 2015) or has a wider taxonomic scope (e.g., angiosperms, Johnson et al, 2019;Zingiberales, Sass et al, 2016;eudicots, Stull et al, 2013); 3) the targeted genome i.e., nuclear (de Sousa et al, 2014;Mandel et al, 2014;Grover et al, 2015) or plastid (Stull et al, 2013). The mitochondrial genome has only begun to be targeted for angiosperm phylogenomic studies (Li et al, 2019). Due to the relatively small size of the plastid genome and its relatively high copy number per cell, assembling complete plastomes (Stull et al, 2013;Sass et al, 2016) or large portions of them (Heyduk et al, 2016) can easily be achieved.…”

Section: Introductionmentioning

confidence: 99%

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum

Mendoza

Jost

Hágsater³

et al. 2020

Front. Plant Sci.

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Universal angiosperm enrichment probe sets designed to enrich hundreds of putatively orthologous nuclear single-copy loci are increasingly being applied to infer phylogenetic relationships of different lineages of angiosperms at a range of evolutionary depths. Studies applying such probe sets have focused on testing the universality and performance of the target nuclear loci, but they have not taken advantage of off-target data from other genome compartments generated alongside the nuclear loci. Here we do so to infer phylogenetic relationships in the orchid genus Epidendrum and closely related genera of subtribe Laeliinae. Our aims are to: 1) test the technical viability of applying the plant anchored hybrid enrichment (AHE) method (Angiosperm v.1 probe kit) to our focal group, 2) mine plastid protein coding genes from off-target reads; and 3) evaluate the performance of the target nuclear and off-target plastid loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. Phylogenetic relationships were inferred from the nuclear data set through coalescent summary and site-based methods, whereas plastid loci were analyzed in a concatenated partitioned matrix under maximum likelihood. The usefulness of target and flanking non-target nuclear regions and plastid loci was assessed through the estimation of their phylogenetic informativeness. Our study successfully applied the plant AHE probe kit to Epidendrum, supporting the universality of this kit in angiosperms. Moreover, it demonstrated the feasibility of mining plastome loci from off-target reads generated with the Angiosperm v.1 probe kit to obtain additional, uniparentally inherited sequence data at no extra sequencing cost. Our analyses detected some strongly supported incongruences between nuclear and plastid data sets at shallow divergences, an indication of potential lineage sorting, hybridization, or introgression events in the group. Lastly, we found that the per site phylogenetic informativeness of the ycf1 plastid gene surpasses that of all

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“…Recently, implementation of high-throughput DNA sequencing methods has expanded the number of DNA regions available for phylogenetic inference, but as with the earlier studies there has been a continuing focus on plastid genes (Edger et al, 2018; Li, Li, et al, 2019) and plastomes (Ross et al, 2016; Guo et al, 2017; Li, Yi, et al, 2019). The rapid growth of organellar phylogenomic studies is an evident trend in many plant families including Araceae (Henriquez et al, 2014), Berberidaceae: (Sun et al, 2018), Lauraceae (Song et al, 2020), Leguminosae (Zhang et al, 2020) and Orchidaceae (Givnish et al, 2015) due to the relative ease with which they are generated: parallel sequencing at shallow coverage (less than 1X) of genomic library preparations derived from recent or historical plant material can yield millions of organellar DNA sequencing reads for hundreds of individuals.…”

Section: Introductionmentioning

confidence: 99%

Hundreds of nuclear and plastid loci yield insights into orchid relationships

Pérez‐Escobar

Dodsworth

Bogarín³

et al. 2020

Preprint

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Premise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

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Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes

Cited by 85 publications

References 77 publications

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum

Hundreds of nuclear and plastid loci yield insights into orchid relationships

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