A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

Sanderson, Brian J.; DiFazio, Stephen P.; Cronk, Quentin; Ma, Tao; Olson, Matthew S.

doi:10.1002/aps3.11394

Cited by 12 publications

(15 citation statements)

References 49 publications

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“…The relative cost effectiveness and the fact that it works well also with degraded DNA, which is common among extractions of herbarium specimens, are some benefits of this approach ( McKain et al, 2018 ; Johnson et al, 2019 ). The probe set used may be specifically designed for the group of study (e.g., Vatanparast et al, 2018 ; Sanderson et al, 2020 ) or designed to be universally applicable across larger groups such as the Angiosperms353 probe kit ( Johnson et al, 2019 ). The large amount and heterogeneity of the data generated for phylogenomic studies do, however, not come without challenges.…”

Section: Introductionmentioning

confidence: 99%

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

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Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.

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Section: Introductionmentioning

confidence: 99%

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

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“…Target capture has been successfully applied to resolve phylogenies in diverse groups, from arthropods such as bees ( Xylocopa , Blaimer et al, 2016 ; Apidae, Bossert et al, 2019 ) and Araneae (Hexathelidae, Hedin et al, 2018 ) to mammals (Cetacea, McGowen et al, 2020 ), and in numerous plant groups ( Heuchera , Folk et al, 2015 ; Gesneriaceae, Ogutcen et al, 2021 ; Zingiberales, Sass et al, 2016 to name a few). The method's utility for studies at microevolutionary scales has been to date marginally explored, but several studies have pointed to the ability to analyse genomic diversity and estimate population genomic parameters (Choquet et al, 2019 ; Christmas et al, 2017 ; Derrien & Ramos‐Onsins, 2020 ; de La Harpe et al, 2019 ; Sanderson et al, 2020 ). Nonetheless, the development of probes for target enrichment may pose several challenges: first, the need to identify regions conserved enough to ensure recovery, yet polymorphic enough to provide ample information (Soto‐Gomez et al, 2019 ; Villaverde et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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

Yardeni

Viruel

Paris

et al. 2021

Molecular Ecology Resources

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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.

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“…This result shows how the bait set is robust to capture a large number of genes, even when the enrichment reaction did not meet expectations (e.g., for G. aesculifolia with 4.4% of on-target reads). Here we applied a great depth of sequence, higher than that applied in other studies (e.g., Soto Gomez et al, 2019 ; Jantzen et al, 2020 ; Sanderson et al, 2020 ; Eserman et al, 2021 ). The sequencing depth and laboratory protocols applied during library preparation and enrichment reaction are relevant variables controlling the number of reads on target, the number of genes recovered, or the total length of the genes compared to the reference ( Johnson et al, 2016 ; Anderman et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae

et al. 2023

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The plant family Bignoniaceae is a conspicuous and charismatic element of the tropical flora. The family has a complex taxonomic history, with substantial changes in the classification of the group during the past two centuries. Recent re-classifications at the tribal and generic levels have been largely possible by the availability of molecular phylogenies reconstructed using Sanger sequencing data. However, our complete understanding of the systematics, evolution, and biogeography of the family remains incomplete, especially due to the low resolution and support of different portions of the Bignoniaceae phylogeny. To overcome these limitations and increase the amount of molecular data available for phylogeny reconstruction within this plant family, we developed a bait kit targeting 762 nuclear genes, including 329 genes selected specifically for the Bignoniaceae; 348 genes obtained from the Angiosperms353 with baits designed specifically for the family; and, 85 low-copy genes of known function. On average, 77.4% of the reads mapped to the targets, and 755 genes were obtained per species. After removing genes with putative paralogs, 677 loci were used for phylogenetic analyses. On-target genes were compared and combined in the Exon-Only dataset, and on-target + off-target regions were combined in the Supercontig dataset. We tested the performance of the bait kit at different taxonomic levels, from family to species-level, using 38 specimens of 36 different species of Bignoniaceae, representing: 1) six (out of eight) tribal level-clades (e.g., Bignonieae, Oroxyleae, Tabebuia Alliance, Paleotropical Clade, Tecomeae, and Jacarandeae), only Tourrettieae and Catalpeae were not sampled; 2) all 20 genera of Bignonieae; 3) seven (out of nine) species of Dolichandra (e.g., D. chodatii, D. cynanchoides, D. dentata, D. hispida, D. quadrivalvis, D. uncata, and D. uniguis-cati), only D. steyermarkii and D. unguiculata were not sampled; and 4) three individuals of Dolichandra unguis-cati. Our data reconstructed a well-supported phylogeny of the Bignoniaceae at different taxonomic scales, opening new perspectives for a comprehensive phylogenetic framework for the family as a whole.

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A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

Cited by 12 publications

References 49 publications

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

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

A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae

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