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Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods. Mol Phylogenet Evol 2023; 178:107666. [PMID: 36384185 DOI: 10.1016/j.ympev.2022.107666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND AIMS A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. METHODS In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. KEY RESULTS Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. CONCLUSIONS Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.
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Hassemer G, Gardner EM, Rønsted N. Plantago campestris (Plantaginaceae), a rare new species from southern Brazil, supported by phylogenomic and morphological evidence. PeerJ 2021; 9:e11848. [PMID: 34527433 PMCID: PMC8401749 DOI: 10.7717/peerj.11848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/02/2021] [Indexed: 11/29/2022] Open
Abstract
High-throughput sequencing, when combined with taxonomic expertise, is a powerful tool to refine and advance taxonomic classification, including at the species level. In the present work, a new species, Plantago campestris, is described out of the P. commersoniana species complex, based on phylogenomic and morphological evidence. The main morphological characters that distinguish the new species from P. commersoniana are the glabrous posterior sepals and the slightly broader leaves. The new species is known from only three localities, all in natural high-elevation grasslands in Paraná and Santa Catarina states, southern Brazil. According to the IUCN criteria new species should be assessed as Endangered (EN). We present field photographs of P. campestris and related species, and we provide an identification key to the species previously included within the circumscription of P. commersoniana.
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Affiliation(s)
- Gustavo Hassemer
- Câmpus de Três Lagoas, Universidade Federal do Mato Grosso do Sul, Três Lagoas, Mato Grosso do Sul, Brazil
| | - Elliot M Gardner
- National Tropical Botanical Garden, Kalãheo, HI, United States of America.,International Center for Tropical Botany, Florida International University, Miami, FL, United States of America
| | - Nina Rønsted
- National Tropical Botanical Garden, Kalãheo, HI, United States of America
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Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, Jabaily RS. The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PHYTOKEYS 2020; 152:27-104. [PMID: 32733134 PMCID: PMC7360637 DOI: 10.3897/phytokeys.152.49604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Close scrutiny of Goodenia (Goodeniaceae) and allied genera in the 'Core Goodeniaceae' over recent years has clarified our understanding of this captivating group. While expanded sampling, sequencing of multiple regions, and a genome skimming reinforced backbone clearly supported Goodenia s.l. as monophyletic and distinct from Scaevola and Coopernookia, there appears to be no synapomorphic characters that uniquely characterise this morphologically diverse clade. Within Goodenia s.l., there is strong support from nuclear, chloroplast and mitochondrial data for three major clades (Goodenia Clades A, B and C) and various subclades, which lead to earlier suggestions for the possible recognition of these as distinct genera. Through ongoing work, it has become evident that this is impractical, as conflict remains within the most recently diverged Clade C, likely due to recent radiation and incomplete lineage sorting. In light of this, it is proposed that a combination of morphological characters is used to circumscribe an expanded Goodenia that now includes Velleia, Verreauxia, Selliera and Pentaptilon, and an updated infrageneric classification is proposed to accommodate monophyletic subclades. A total of twenty-five new combinations, three reinstatements, and seven new names are published herein including Goodenia subg. Monochila sect. Monochila subsect. Infracta K.A.Sheph. subsect. nov. Also, a type is designated for Goodenia subg. Porphyranthus sect. Ebracteolatae (K.Krause) K.A.Sheph. comb. et stat. nov., and lectotypes or secondstep lectotypes are designated for a further three names.
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Affiliation(s)
- Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation & Attractions, Kensington, WA 6151, AustraliaWestern Australian HerbariumKensingtonAustralia
| | - Brendan J. Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1700, Canberra, ACT, 2601, AustraliaAustralian National HerbariumCanberraAustralia
| | - Eden A. Johnson
- Department of Biology, University of Mississippi, Oxford, MS 38677, USAUniversity of MississippiOxfordUnited States of America
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, Turlock, CA 95382, USACalifornia State UniversityTurlockUnited States of America
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USAUniversity of FloridaGainesvilleUnited States of America
| | - Rachel S. Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USAColorado CollegeColorado SpringsUnited States of America
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Köhler M, Reginato M, Souza-Chies TT, Majure LC. Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies. FRONTIERS IN PLANT SCIENCE 2020; 11:729. [PMID: 32636853 PMCID: PMC7317007 DOI: 10.3389/fpls.2020.00729] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/22/2023]
Abstract
Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.
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Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Lucas C Majure
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, United States
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Hassemer G, Bruun-Lund S, Shipunov AB, Briggs BG, Meudt HM, Rønsted N. The application of high-throughput sequencing for taxonomy: The case of Plantago subg. Plantago (Plantaginaceae). Mol Phylogenet Evol 2019; 138:156-173. [DOI: 10.1016/j.ympev.2019.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/11/2022]
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Herrando-Moraira S, Calleja JA, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Massó S, Montes-Moreno N, Roquet C, Sáez L, Sennikov A, Susanna A, Vilatersana R. Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework. Mol Phylogenet Evol 2019; 137:313-332. [DOI: 10.1016/j.ympev.2019.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/04/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023]
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Pizarro D, Divakar PK, Grewe F, Leavitt SD, Huang JP, Dal Grande F, Schmitt I, Wedin M, Crespo A, Lumbsch HT. Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0407-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Fonseca LHM, Lohmann LG. Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae). Mol Phylogenet Evol 2018; 123:1-15. [DOI: 10.1016/j.ympev.2018.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
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Jabaily RS, Shepherd KA, Michener PS, Bush CJ, Rivero R, Gardner AG, Sessa EB. Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae). Mol Phylogenet Evol 2018; 127:502-512. [PMID: 29758275 DOI: 10.1016/j.ympev.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/22/2018] [Accepted: 05/07/2018] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- Rachel S Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USA; Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia.
| | | | - Caroline J Bush
- Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Rodrigo Rivero
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Department of Natural Resources and Environmental Management, University of Hawaii- Mānoa, Honolulu, HI 96822, USA.
| | - Andrew G Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, CA 95382, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA.
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700042. [PMID: 29109919 PMCID: PMC5664964 DOI: 10.3732/apps.1700042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2017] [Indexed: 05/20/2023]
Abstract
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.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A. Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
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Fonseca LHM, Lohmann LG. Plastome Rearrangements in the " Adenocalymma-Neojobertia" Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications. FRONTIERS IN PLANT SCIENCE 2017; 8:1875. [PMID: 29163600 PMCID: PMC5672021 DOI: 10.3389/fpls.2017.01875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 10/16/2017] [Indexed: 05/02/2023]
Abstract
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes. Plastomes were assembled using selected plastid reads and de novo approach with SPAdes. The 10 assembled genomes were analyzed in a phylogenetic context using five different partition schemes: (1) 91 protein-coding genes ("coding"); (2) 76 introns and spacers with alignment manually edited ("non-coding edited"); (3) 76 non-coding regions with poorly aligned regions removed using T-Coffee ("non-coding filtered"); (4) 91 coding regions plus 76 non-coding regions edited ("coding + non-coding edited"); and, (5) 91 protein-coding regions plus the 76 filtered non-coding regions ("coding + non-coding filtered"). Fragmented regions were aligned using Mafft. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Criteria (BC). The analyses of the individual plastomes consistently recovered an expansion of the Inverted Repeated (IRs) regions and a compression of the Small Single Copy (SSC) region. Major genomic translocations were observed at the Large Single Copy (LSC) and IRs. ML phylogenetic analyses of the individual datasets led to the same topology, with the exception of the analysis of the "non-coding filtered" dataset. Overall, relationships were strongly supported, with the highest support values obtained through the analysis of the "coding + non-coding edited" dataset. Four regions at the LSC, SSC, and IR were selected for primer development. The "Adenocalymma-Neojobertia" clade shows an unusual pattern of plastid structure variation, including four major genomic translocations. These rearrangements challenge the current view of conserved plastid genome architecture in terms of gene order. It also complicates both genomic assemblies using reference genomes and sequence alignments using whole plastomes. Therefore, strategies that employ de novo assemblies and manual evaluation of sequence alignments are required to prevent assembly and alignment errors.
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Reginato M, Neubig KM, Majure LC, Michelangeli FA. The first complete plastid genomes of Melastomataceae are highly structurally conserved. PeerJ 2016; 4:e2715. [PMID: 27917315 PMCID: PMC5131623 DOI: 10.7717/peerj.2715] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 11/20/2022] Open
Abstract
Background In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. Methods Genome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenetic inference was performed using Maximum Likelihood on six different data sets, where putative biases were taken into account. Summary statistics were generated for all introns and intergenic spacers with suitable size for polymerase chain reaction (PCR) amplification and used to rank the markers by phylogenetic information. Results The majority of the plastomes sampled are conserved in gene content and order, as well as in sequence length and GC content within plastid regions and sequence classes. Departures include the putative presence of rps16 and rpl2 pseudogenes in some plastomes. Phylogenetic analyses of the majority of the schemes analyzed resulted in the same topology with high values of bootstrap support. Although there is still uncertainty in some relationships, in the highest supported topologies only two nodes received bootstrap values lower than 95%. Discussion Melastomataceae plastomes are no exception for the general patterns observed in the genomic structure of land plant chloroplasts, being highly conserved and structurally similar to most other Myrtales. Despite the fact that the full plastome phylogeny shares most of the clades with the previously widely used and reduced data set, some changes are still observed and bootstrap support is higher. The plastome data set presented here is a step towards phylogenomic analyses in the Melastomataceae and will be a useful resource for future studies.
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Affiliation(s)
- Marcelo Reginato
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
| | - Kurt M Neubig
- Department of Plant Biology, Southern Illinois University of Carbondale , Carbondale, Illinois , United States
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden , Phoenix, Arizona , United States
| | - Fabian A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden , Bronx, New York , United States
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Gardner AG, Fitz Gerald JN, Menz J, Shepherd KA, Howarth DG, Jabaily RS. Characterizing Floral Symmetry in the Core Goodeniaceae with Geometric Morphometrics. PLoS One 2016; 11:e0154736. [PMID: 27148960 PMCID: PMC4858217 DOI: 10.1371/journal.pone.0154736] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
Core Goodeniaceae is a clade of ~330 species primarily distributed in Australia. Considerable variation in flower morphology exists within this group and we aim to use geometric morphometrics to characterize this variation across the two major subclades: Scaevola sensu lato (s.l.) and Goodenia s.l., the latter of which was hypothesized to exhibit greater variability in floral symmetry form. We test the hypothesis that floral morphological variation can be adequately characterized by our morphometric approach, and that discrete groups of floral symmetry morphologies exist, which broadly correlate with subjectively determined groups. From 335 images of 44 species in the Core Goodeniaceae, two principal components were computed that describe >98% of variation in all datasets. Increasing values of PC1 ventralize the dorsal petals (increasing the angle between them), whereas increasing values of PC2 primarily ventralize the lateral petals (decreasing the angle between them). Manipulation of these two morphological “axes” alone was sufficient to recreate any of the general floral symmetry patterns in the Core Goodeniaceae. Goodenia s.l. exhibits greater variance than Scaevola s.l. in PC1 and PC2, and has a significantly lower mean value for PC1. Clustering clearly separates fan-flowers (with dorsal petals at least 120° separated) from the others, whereas the distinction between pseudo-radial and bilabiate clusters is less clear and may form a continuum rather than two distinct groups. Transitioning from the average fan-flower to the average non-fan-flower is described almost exclusively by PC1, whereas PC2 partially describes the transition between bilabiate and pseudo-radial morphologies. Our geometric morphometric method accurately models Core Goodeniaceae floral symmetry diversity.
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Affiliation(s)
- Andrew G. Gardner
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
- * E-mail:
| | - Jonathan N. Fitz Gerald
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - John Menz
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
| | - Kelly A. Shepherd
- Science and Conservation Division, Department of Parks and Wildlife, Kensington, Western Australia, Australia
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, Queens, New York, United States of America
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee, United States of America
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