Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

BACKGROUND

Despite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana.

RESULTS

Our pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments, and (4) the topology of the nuclear and plastid phylogenies. Additionally, the simulated reads derived from the genome of Arabidopsis thaliana were used to evaluate the accuracy and completeness of the recovered loci. In terms of computation time, locus recovery per sample, and informative sites, Captus outperforms HybPiper and SECAPR. The resulting topologies of Captus and SECAPR are identical for coalescent trees but differ when trees are inferred from concatenated alignments. The HybPiper phylogeny is similar to Captus in both methods. The nuclear genes recover a deep split of Thladiantha in two clades, but this is not supported by the plastid data.

CONCLUSIONS

Captus is the best choice among the three pipelines in terms of computation time and locus recovery. Even though there is no significant topological difference between the Thladiantha species trees produced by the three pipelines, Captus yields a higher number of gene trees in agreement with the topology of the species tree (i.e., fewer genes in conflict with the species tree topology).

Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing

BACKGROUND AND AIMS

Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe.

METHODS

We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches.

KEY RESULTS

Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae.

CONCLUSIONS

We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.

A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

Premise

Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking.

Methods

Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.

Results

We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.

Discussion

Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

Target capture and genome skimming for plant diversity studies

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets. To address these challenges, we developed target capture probes for genomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built the general purpose bioinformatic pipeline CaptureAl. Phylogenomic analyses of Malagasy Dalbergia species yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatic resources, including the Fabaceae1005 and Dalbergia2396 probe sets, will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae)

Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.

Utilizing paralogs for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data

The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogs for phylogenetic reconstruction. We developed a novel approach of detecting paralogs and utilizing them for phylogenetic tree inference, by retrieving both ortho- and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes. Discriminating between orthologs and paralogs reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the datasets, which was highest for the Malinae. Overall, retrieving paralogs for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high.

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

Background

Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups.

Methods

We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies.

Results

We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations

Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

PREMISE

Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses.

METHODS

We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets.

RESULTS

Our results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways.

DISCUSSION

Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.

How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.