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29 results for “Goodeniaceae”
Data from: Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1–C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.
Data from: Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)
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Supplementary material 1 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Summary of GenBank accession numbers, Taxon names, Project numbers, Herbarium Accession numbers, voucher collectors and collection numbers, phylogenetic position and taxonomy and classification according to Shepherd et al.
Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. Results: Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. Discussion: Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
FIGURE 2 in Scaevola rialagartensis (Goodeniaceae), a new species from coastal sand dunes of Rio Lagartos, Yucatan, Mexico
FIGURE 2. Illustration of Scaevola rialagartensis. a, portion of the habit; b, branch with flowers and fruits; c, detail of the leaf; d, portion of the inflorescence; e, flower with stigma details; f, stamen, g, portion of the infrutescence; h, fruit, longitudinal section; i, seed covered with the aril; j, seeds. Illustration by Edmundo Saavedra based on the holotype specimen G. Castillo-Campos & J.J. Pale P. 29321.
FIGURE 3 in Scaevola rialagartensis (Goodeniaceae), a new species from coastal sand dunes of Rio Lagartos, Yucatan, Mexico
FIGURE 3. Scaevola rialagartensis Cast.-Campos sp. nov. in its habitat. a) shrub lying on the sand dune and parasitized by Cassytha filiformis L.; b) branch with inflorescences, flowers in anthesis, and revolute leaves. (Photos G. Castillo-Campos).
Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes
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Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies
Open the record for dataset details and reuse information.
Supplementary material 8 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade A cpDNA (trnL-F, matK) alignment
Supplementary material 11 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade B nrITS alignment
Supplementary material 12 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade C cpDNA (trnL-F, matK) alignment
Supplementary material 10 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade B cpDNA (trnL-F, matK) alignment
Supplementary material 9 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade A nrITS alignment
Figure 7 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Figure 7 Goodenia Clade B_2 phylogeny from combined nrDNA + cpDNA sequence data and exemplar taxa of major subclades. Topology is 50% majority rule cladogram from the partitioned Bayesian inference analysis. Support values above the branches are Bayesian posterior probabilities and below are maximum likelihood bootstrap values. Branch colour corresponds with support values and taxon colour corresponds to the taxonomic classification of Carolin et al. (1992). For updated taxonomy from this paper, see Tables 1, 2. Taxa represented by multiple accessions are distinguished by project code numbers as listed in Suppl. material 1. AG. leiospermaBG. heteromeraCG. heterochilaDG. muellerianaEG. macroplectraFG. glandulosaGG. odonnelliiHG. pilosaIG. armstrongiana (White form). Images: C. Nieminski (A, G–I); Seeds of South Australia (B, C, F); A. Perkins (D); K.R. Thiele (E).
Figure 1 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Figure 1 Summary of broad relationships in Goodeniaceae from Jabaily et al. (2012) based on a 50% majority-rule cladogram from a partitioned Bayesian inference analysis of trnL-F and matK, with additional bootstrap values from separate parsimony and maximum likelihood analyses (values above branches are Bayesian posterior probabilities, values below branches are maximum likelihood bootstrap). Left inset – Coopernookia strophiolata showing the unique indusium pollen presenter (red arrow) that is diagnostic for the family. Voucher: K.R. Thiele 3710. Image: K.R. Thiele.
Figure 4 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Figure 4 Diagramatic sections of ovaries (l.s.) modified from Carolin (1959). From left–right Velleia, Goodenia, Verreauxia, and Scaevola, showing fusion of floral parts and structure of the incomplete locules and placentation of ovules.
Supplementary material 3 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade A nrITS phylogeny
Supplementary material 4 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Goodenia Clade B cpDNA (trnL-F, matK) phylogeny
Figure 3 from: Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, S. Jabaily R (2020) The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PhytoKeys 152: 27-104. https://doi.org/10.3897/phytokeys.152.49604
Figure 3 Characterisation of inflorescence structure in Goodenias.l. modified from Carolin (1967a) with his corresponding Bauplan 'Type' concepts stated were applicable and phylogenetic position for exemplar species given in brackets; MI = main inflorescence, EZ = enrichment zone, V = vegetative zone. A Form A (Type 1) is a thyrse with leafy bracts and bracteoles e.g. Goodenia ovata (Goodenia I) or (Type 2) 1(–2)-flowered raceme with leafy bracts and bracteoles e.g. G. laevis (Goodenia I) (inset) B Form B (Type 5) is a basal rosette with leafy bracts and bracteoles e.g. G. hederacea (Goodenia II) C Form C (no Type) with flowers solitary in leaf axils, leafy bracts and bracteoles e.g. G. convexa (Goodenia II) D Form D (no Type) flowers solitary in leaf axils with leafy bracts, bracteoles absent e.g. G. pumilo (Porphyranthus I) E Form E (Type 4) a basal rosette, bracteoles, with leafy bracteose bracts and either a panicle-like form e.g. G. paniculata, raceme e.g. G. gracilis (Porphyranthus II) (inset above) or a thyrse e.g. G. pterigosperma (Coeruleae) (inset below) F Form F (Type 6) with ebracteolate racemes and leafy bracts e.g. G. hispida (Ebracteolatae II), (Type 7) non-leafy bracts e.g. G. cusackiana (Ebracteolatae I) (inset above), or (Type 8) a subumbel e.g. G . pulchella (Ebracteolatae I) (inset below) G Form G (Type 3) represented by a thyrse with reduced bracts and bracteoles e.g. G. scapigera (Monochila) and H Form H (Velleia Type) is a compound dichasium with leafy bracts and bracteoles e.g Velleia lyrata (Velleia).
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