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Tanglegram comparisons of phylogenies obtained using a supermatrix approach and IQ-TREE, and a coalescent approach and ASTRAL-III of the Exon-Only dataset. The supermatrix result includes ultra-fast bootstrap proportion (UFBoot) support values. The coalescent result is labeled with local posterior probabilities (LPP). Values above branches with maximum support of the UFBoot and LPP are not shown. Branches labeled on the supermatrix tree are discussed in the text. Shaded boxes enclose the entire Bignoniaceae family; the tribe Bignoniaeae; and the genus Dolichandra.
Source publication
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 ph...
Citations
... Alignment sets with intron sequences were between three to six times larger than the exon data, and thus by depth the intron data could have provided resolution that was not available in the exon alignments (Table S4). Also, mutation rates from these flanking regions are thought to be closer to neutral substitution rates compared to the potentially regulated exon regions, meaning that the intron data may contain more relevant information for distinguishing shallower evolutionary relationships (Faircloth et al., 2012;Johnson et al., 2016;Ogutcen et al., 2021;Fonseca et al., 2023). If this is the case, the divergence of the two Celmisia groups may have been retained in the intron regions but obscured in the exon regions. ...
... This approach has been profitable in groups such as Bromeliaceae (Yardeni et al., 2022), Ochnaceae (Shah et al., 2021), Malinae (Rosaceae) (Ufimov et al. 2021), the centropogonid clade (Campanulaceae) (Lagomarsino et al., 2022), Eucalyptus L'Hér. (Myrtaceae) , Bignoniaceae (Fonseca et al., 2023), and Cactaceae (Acha and Majure, 2022). ...
... In plants, "universal" probe sets have been developed for gene capture in flagellate land plants (Breinholt et al., 2021) and angiosperms (Johnson et al., 2019). Family-specific probe sets have been successfully developed for many different plant families, such as Annonaceae (Couvreur et al., 2019), Fabaceae (Koenen et al., 2020), Ochnaceae (Shah et al., 2021), Bromeliaceae (Yardeni et al., 2022), Bignoniaceae (Fonseca et al., 2023), and others. ...
Premise
A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.
Methods
In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.
Results
The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.
Discussion
This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant‐targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.
... Universal kits targeting all angiosperms are available (Buddenhagen et al., 2016;Johnson et al., 2019;Waycott et al., 2021), as well as customized bait kits designed for plant families such as Annonaceae (Couvreur et al., 2019), Apocynaceae (Weitemier et al., 2014), Asteraceae (Mandel et al., 2014), Bignoniaceae (Fonseca et al., 2023), Gesneriaceae (Ogutcen et al., 2021), Ochnaceae (Schneider et al., 2020) and Orchidaceae (Eserman et al., 2021); or more inclusive clades such as Begonia L. (Begoniaceae;Michael et al., 2022), Buddleja L. ...
... Rather than comparing, a fruitful approach is the merging of both universal and specific gene sets in a single bait kit (Hendricks et al., 2021). By doing so, it is possible to combine the versatility of universal and the efficiency of specific bait kits in a single framework, making available as many genes as possible for phylogenetic or population studies (Mandel et al., 2014;Eserman et al., 2021;Fonseca et al., 2023). ...
... ; https://doi.org/10.1101/2023.11.16.567445 doi: bioRxiv preprint limitation for some species and clades, as was clear in the original publication (Johnson et al., 2019). The maintenance of the Angiosperms353 gene set coupled with clade specific baits is a step forward assuring high recovery values for all the genes in most cases (e.g., Ogutcen et al., 2021;Fonseca et al., 2023). The recovery rate of the new version of the Annonaceae bait kit is extremely high (Figure 1), with a mean value of 798.4 genes or 99.9%, and 776.9 genes assembled at up to 50% per species (Table 1), echoing previous results obtained for Bignoniaceae of 98% (Fonseca et al., 2023). ...
PREMISE: The development of RNA baiting kits for reduced representation approaches of genomic sequencing is popularized, with universal and clade-specific kits for flowering plants available. Here, we provided an updated version of the Annonaceae bait kit targeting 799 low copy genes, known as Annonaceae799.
METHODS: This new version of the kit combines the original 469 genes from the previous version of the Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compared the results obtained using the Original Angiosperms353 kit with our custom approach. Parsimony informative sites (pis) were evaluated for all genes and combined matrices.
RESULTS: The new version of the kit has extremely high rates of gene recovery. On average, 796 genes were recovered per sample, and 777.5 genes recovered with at least 50% of their size. Off-target reads were also obtained. Evaluating size, the proportion of on- and off-target regions, and the number of pis, the genes from the Angiosperms353 usually outperform the genes from the original Annonaceae bait kit.
DISCUSSION: The results obtained show that the new sequences from the Angiosperms353 aggregate variable and putative relevant bases for future studies on species-level phylogenomics, and within species studies. The merging of kits also creates a link between projects and makes available new genes for phylogenetic and populational studies.
... Taxon-specific bait sets include loci chosen for a specific experiment; for example, bait sets might include single-or low-copy loci that are phylogenetically informative independent of their function (e.g., Vatanparast et al., 2018;Ojeda et al., 2019;Soto Gomez et al., 2019;Eserman et al., 2021;Romeiro-Brito et al., 2022). In addition, bait sets might include previously annotated loci with functions relevant to that plant group (Nicholls et al., 2015;Yardeni et al., 2022;Fonseca et al., 2023); for example, the bait set developed for the genus Inga Mill. (ca. ...
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.
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
Species with lianescent habit account for half of the diversity of Bignoniaceae. Recent molecular phylogenetic studies have provided the basis for new circumscriptions of entire liana lineages within tribes Bignonieae and Tecomeae s.s., where only monophyletic taxa are recognized. However, some clades remain without good morphological synapomorphies. In search of features of taxonomic potential, we collected, sectioned, and analyzed the bark of 83 lianescent species of the Bignoniaceae, covering all 20 genera from tribe Bignonieae currently recognized, plus three of the most widely cultivated lianas of Tecomeae s.s. Detailed bark descriptions are given to major lineages within both tribes, following their most recent phylogenetic hypotheses and classifications. Our anatomical studies allowed us to identify 19 potential synapomorphies for large clades or specific genera of lianas, such as the fibrous phloem found in members of the Fridericia Mart. emend L.G.Lohmann and allies clade, the exclusive presence of sclereids in the regular phloem of Pleonotoma Miers, and the presence of radially elongated fibers in Manaosella L.C.Gomes, among others. Using a combination of features, we were able to produce the first bark key to identify genera of lianescent Bignoniaceae. Our work reinforces the importance of bark features for a deeper understanding of taxonomic and phylogenetic relationships among taxa. © Publications scientifiques du Muséum national d’Histoire naturelle, Paris.
