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Zumkeller S, Polsakiewicz M, Knoop V. Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis. Commun Biol 2023; 6:296. [PMID: 36941328 PMCID: PMC10027690 DOI: 10.1038/s42003-023-04659-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.
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Affiliation(s)
- Simon Zumkeller
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Monika Polsakiewicz
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany.
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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Nieves KG, van Ee BW. DNA Barcoding of Adiantum (Pteridaceae: Vittarioideae) in Puerto Rico. CARIBB J SCI 2021. [DOI: 10.18475/cjos.v51i2.a13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Benjamin W. van Ee
- Department of Biology, University of Puerto Rico, Mayagüez, Mayagüez, Puerto Rico
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May MR, Contreras DL, Sundue MA, Nagalingum NS, Looy CV, Rothfels CJ. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity. Syst Biol 2021; 70:1232-1255. [PMID: 33760075 PMCID: PMC8513765 DOI: 10.1093/sysbio/syab020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth-death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.].
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Affiliation(s)
- Michael R May
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
| | - Dori L Contreras
- Department of Paleontology, Perot Museum of Nature and Science, 2201 N. Field Street, Dallas TX 75201, USA
| | - Michael A Sundue
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
- The Pringle Herbarium, University of Vermont, 305 Jeffords Hall, 63 Carrigan Drive, Burlington, VT 05405, USA
| | - Nathalie S Nagalingum
- Department of Botany, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Cindy V Looy
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Carl J Rothfels
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
- University Herbarium, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA
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Irfan M, Jan G, Jan FG, Murad W. Taxonomy and spore morphology of selected taxa of Cheilanthoideae and Pteridoideae (Pteridaceae) from Pakistan. Microsc Res Tech 2021; 84:2867-2882. [PMID: 34121271 DOI: 10.1002/jemt.23845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/23/2021] [Accepted: 05/12/2021] [Indexed: 11/07/2022]
Abstract
Taxonomy and spore morphology of 12 taxa of Cheilanthoideae and Pteridoideae (Pteridaceae, Polypodiales) from Pakistan is illustrated with scanning electron microscopy images based upon the specimens collected from various localities. A total of six genera belong to 12 taxa viz. Actiniopteris radiata, Aleuritopteris albomarginata, A. ancepes, Notholaena himalaica, Oeosporangium nitidulum, O. pteridioides subsp. acrosticum, Onychium cryptogrammoides subsp. cryptogrammoides, O. vermae, Pteris cretica subsp. cretica, P. cretica subsp. laeta, P. vittata subsp. emodi, and P. vittata subsp. vittata were reported. Spore morphology of the taxa was trilete, triangular in proximal and distal view, ellipsoidal and hemicircular in equatorial view, polar proximal and distal surface with cristate, granulose, reticulate, perforate and tuberculate ornamentation.
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Affiliation(s)
- Muhammad Irfan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
- Department of Botany, University of Swabi, Swabi, Pakistan
- Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, Missouri, 63110, USA
| | - Gul Jan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Farzana Gul Jan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Waheed Murad
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
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Irfan M, Jan G, Jan FG, Murad W. Taxonomy and spore morphology of genus Adiantum (Vittarioideae; Pteridaceae) from Pakistan. Microsc Res Tech 2021; 84:2727-2736. [PMID: 34051004 DOI: 10.1002/jemt.23835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022]
Abstract
Taxonomy and spore morphology of genus Adiantum (Vittarioideae; Pteridaceae) from Pakistan is illustrated with scanning electron microscopy images based upon the specimens examined in herbaria of Pakistan, United Kingdom, and United States. A total of five species viz. Adiantum capillus-veneris, A. incisum subsp. incisum, A. pedatum subsp. pedatum, A. tibeticum, and A. venustum were reported with the habitat ecology of the species from Pakistan. Spore morphology of the taxa was trilete, triangular in proximal and distal view, ellipsoidal and hemicircular in equatorial view, polar proximal and distal surface was with tuberculate and granulose ornamentation. HIGHLIGHTS: Taxonomy and spore morphology of five species of Adiantum from Pakistan. Spore trilete, triangular in proximal and distal view with globose and tuberculate surface. Habitat, ecology, and specimens were examined at multiple herbaria for the correct identification of species.
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Affiliation(s)
- Muhammad Irfan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan.,Department of Botany, University of Swabi, Swabi, Pakistan.,Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, Missouri, 63110, USA
| | - Gul Jan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Farzana Gul Jan
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
| | - Waheed Murad
- Department of Botany, Abdul Wali Khan University, Mardan, Pakistan
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Bastos LM, Mynssen CM. Lytoneuron (Pteridaceae) no estado do Rio de Janeiro, Brasil. RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Resumo Lytoneuron está circunscrito a família Pteridaceae (Cheilanthoideae) e foi segregado do gênero Doryopteris s.l. a partir da evidência molecular e morfológica, reconhecido como uma linhagem monofilética. Este estudo se baseia na análise de espécimes ocorrentes no estado do Rio de Janeiro, obtidos no campo e que estão nos acervos dos herbários. Como resultado, são indicadas 11 espécies de Lytoneuron para o estado das quais nove são consideradas endêmicas do Brasil e restritas ao bioma Mata Atlântica (Lytoneuron acutilobum, L. itatiaiense, L. feei, L. ornithopus, L. paradoxum, L. quinquelobatum, L. rosenstockii, L. subsimplex e L. tijucanum). As espécies Lytoneuron quinquelobatum, L. subsimplex e L. tijucanum são conhecidas apenas para o estado Rio de Janeiro. São apresentadas descrições, comentários, ilustrações e uma chave de identificação.
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Affiliation(s)
- Luiza Mendonça Bastos
- Universidade Federal Fluminense, Brasil; Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Brasil
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Wu D, Li L, Ma X, Huang G, Yang C. Morphological and anatomical adaptations to dry, shady environments in Adiantum reniforme var. sinense (Pteridaceae). PeerJ 2020; 8:e9937. [PMID: 33062425 PMCID: PMC7532779 DOI: 10.7717/peerj.9937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/24/2020] [Indexed: 11/20/2022] Open
Abstract
The natural distribution of the rare perennial fern Adiantum reniforme var. sinense (Pteridaceae), which is endemic to shady cliff environments, is limited to small areas of Wanzhou County, Chongqing, China. In this study, we used brightfield and epifluorescence microscopy to investigate the anatomical structures and histochemical features that may allow this species to thrive in shady, dry cliff environments. The A. reniforme var. sinense sporophyte had a primary structure and a dictyostele. The plants of this species had an endodermis, sclerenchyma layers and hypodermal sterome, reflecting an adaption to dry cliff environments. Blades had a thin cuticle and isolateral mesophyll, suggesting a tolerance of shady environments. These characteristics are similar to many sciophyte ferns such as Lygodium japonicum and Pteris multifida. Thus, the morphological and anatomical characteristics of A. reniforme var. sinense identified in this study are consistent with adaptations to shady, dry cliff environments.
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Affiliation(s)
- Di Wu
- Rare Plants Research Institute of Yangtze River, Three Gorges Corporation, Yichang, China
| | - Linbao Li
- Rare Plants Research Institute of Yangtze River, Three Gorges Corporation, Yichang, China
| | - Xiaobo Ma
- Rare Plants Research Institute of Yangtze River, Three Gorges Corporation, Yichang, China
| | - Guiyun Huang
- Rare Plants Research Institute of Yangtze River, Three Gorges Corporation, Yichang, China
| | - Chaodong Yang
- Engineering Research Center of Ecology and Agriculture Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
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Lehtonen S, Poczai P, Sablok G, Hyvönen J, Karger DN, Flores J. Exploring the phylogeny of the marattialean ferns. Cladistics 2020; 36:569-593. [DOI: 10.1111/cla.12419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 01/21/2023] Open
Affiliation(s)
- Samuli Lehtonen
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
| | - Péter Poczai
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
- OEB and ViPS University of Helsinki PO Box 65 FI‐00014 Helsinki Finland
| | - Dirk N. Karger
- Biodiversity Unit University of Turku FI‐20014 Turku Finland
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
| | - Jorge Flores
- Finnish Museum of Natural History (Botany) University of Helsinki PO Box 7 FI‐00014 Helsinki Finland
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10
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Bell D, Lin Q, Gerelle WK, Joya S, Chang Y, Taylor ZN, Rothfels CJ, Larsson A, Villarreal JC, Li FW, Pokorny L, Szövényi P, Crandall-Stotler B, DeGironimo L, Floyd SK, Beerling DJ, Deyholos MK, von Konrat M, Ellis S, Shaw AJ, Chen T, Wong GKS, Stevenson DW, Palmer JD, Graham SW. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. AMERICAN JOURNAL OF BOTANY 2020; 107:91-115. [PMID: 31814117 DOI: 10.1002/ajb2.1397] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
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Affiliation(s)
- David Bell
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
- Royal Botanic Garden, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Wesley K Gerelle
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Steve Joya
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ying Chang
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Z Nathan Taylor
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California Berkeley, Berkeley, California, 94702, USA
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Juan Carlos Villarreal
- Department of Biology, Université Laval, Québec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | | | - Lisa DeGironimo
- Department of Biology, College of Arts and Science, New York University, New York, New York, 10003, USA
| | - Sandra K Floyd
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Matt von Konrat
- Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Shona Ellis
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, China
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | | | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
- UBC Botanical Garden and Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, British Columbia, V6T 1Z4, Canada
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11
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Robison TA, Grusz AL, Wolf PG, Mower JP, Fauskee BD, Sosa K, Schuettpelz E. Mobile Elements Shape Plastome Evolution in Ferns. Genome Biol Evol 2018; 10:2558-2571. [PMID: 30165616 PMCID: PMC6166771 DOI: 10.1093/gbe/evy189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
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Affiliation(s)
| | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
| | - Paul G Wolf
- Department of Biology, Utah State University
| | - Jeffrey P Mower
- Department of Agronomy, Center for Plant Science Innovation, University of Nebraska
| | | | | | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
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12
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Further progress towards the delimitation of Cheilanthes (Cheilanthoideae, Pteridaceae), with emphasis on South American species. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0366-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Wolf PG, Robison TA, Johnson MG, Sundue MA, Testo WL, Rothfels CJ. Target sequence capture of nuclear-encoded genes for phylogenetic analysis in ferns. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01148. [PMID: 30131890 PMCID: PMC5991577 DOI: 10.1002/aps3.1148] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/04/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Until recently, most phylogenetic studies of ferns were based on chloroplast genes. Evolutionary inferences based on these data can be incomplete because the characters are from a single linkage group and are uniparentally inherited. These limitations are particularly acute in studies of hybridization, which is prevalent in ferns; fern hybrids are common and ferns are able to hybridize across highly diverged lineages, up to 60 million years since divergence in one documented case. However, it not yet clear what effect such hybridization has on fern evolution, in part due to a paucity of available biparentally inherited (nuclear-encoded) markers. METHODS We designed oligonucleotide baits to capture 25 targeted, low-copy nuclear markers from a sample of 24 species spanning extant fern diversity. RESULTS Most loci were successfully sequenced from most accessions. Although the baits were designed from exon (transcript) data, we successfully captured intron sequences that should be useful for more focused phylogenetic studies. We present phylogenetic analyses of the new target sequence capture data and integrate these into a previous transcript-based data set. DISCUSSION We make our bait sequences available to the community as a resource for further studies of fern phylogeny.
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Affiliation(s)
- Paul G. Wolf
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Tanner A. Robison
- Ecology Center and Department of BiologyUtah State UniversityLoganUtah84322USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Michael A. Sundue
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Weston L. Testo
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermont05405USA
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative BiologyUniversity of CaliforniaBerkeleyCalifornia94720USA
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14
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Ma PF, Vorontsova MS, Nanjarisoa OP, Razanatsoa J, Guo ZH, Haevermans T, Li DZ. Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics. BMC PLANT BIOLOGY 2017; 17:260. [PMID: 29268709 PMCID: PMC5740905 DOI: 10.1186/s12870-017-1199-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. RESULTS Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. CONCLUSIONS Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect.
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Affiliation(s)
- Peng-Fei Ma
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Maria S. Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB UK
| | | | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, BP 4096, Antananarivo 101, Madagascar
| | - Zhen-Hua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Thomas Haevermans
- Institut de Systématique, Évolution, Biodiversité (ISYEB) UMR 7205 Centre national de la recherche scientifique - Muséum national d’histoire naturelle - École Pratique des Hautes Études – Université Pierre et Marie Curie, Sorbonne Universités, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
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15
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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16
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A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
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17
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Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae). PLoS One 2016; 11:e0160611. [PMID: 27603700 PMCID: PMC5014338 DOI: 10.1371/journal.pone.0160611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.
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18
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Grusz AL, Rothfels CJ, Schuettpelz E. Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. BMC Genomics 2016; 17:692. [PMID: 27577050 PMCID: PMC5006594 DOI: 10.1186/s12864-016-3034-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/22/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection. RESULTS We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution. CONCLUSIONS Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.
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Affiliation(s)
- Amanda L. Grusz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
- Department of Biology, University of Minnesota Duluth, 1035 Kirby Drive, Duluth, MN 55812 USA
| | - Carl J. Rothfels
- Department of Integrative Biology, University of California Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720-2466 USA
| | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013-7012 USA
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19
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Zumkeller SM, Knoop V, Knie N. Convergent Evolution of Fern-Specific Mitochondrial Group II Intron atp1i361g2 and Its Ancient Source Paralogue rps3i249g2 and Independent Losses of Intron and RNA Editing among Pteridaceae. Genome Biol Evol 2016; 8:2505-19. [PMID: 27492234 PMCID: PMC5010907 DOI: 10.1093/gbe/evw173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial intron patterns are highly divergent between the major land plant clades. An intron in the atp1 gene, atp1i361g2, is an example for a group II intron specific to monilophytes (ferns). Here, we report that atp1i361g2 is lost independently at least 4 times in the fern family Pteridaceae. Such plant organelle intron losses have previously been found to be accompanied by loss of RNA editing sites in the flanking exon regions as a consequence of genomic recombination of mature cDNA. Instead, we now observe that RNA editing events in both directions of pyrimidine exchange (C-to-U and U-to-C) are retained in atp1 exons after loss of the intron in Pteris argyraea/biaurita and in Actiniopteris and Onychium We find that atp1i361g2 has significant similarity with intron rps3i249g2 present in lycophytes and gymnosperms, which we now also find highly conserved in ferns. We conclude that atp1i361g2 may have originated from the more ancestral rps3i249g2 paralogue by a reverse splicing copy event early in the evolution of monilophytes. Secondary structure elements of the two introns, most characteristically their domains III, show strikingly convergent evolution in the monilophytes. Moreover, the intron paralogue rps3i249g2 reveals relaxed evolution in taxa where the atp1i361g2 paralogue is lost. Our findings may reflect convergent evolution of the two related mitochondrial introns exerted by co-evolution with an intron-binding protein simultaneously acting on the two paralogues.
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Affiliation(s)
- Simon Maria Zumkeller
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Nils Knie
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
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20
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Li FW, Kuo LY, Pryer KM, Rothfels CJ. Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content. Genome Biol Evol 2016; 8:2452-8. [PMID: 27401175 PMCID: PMC5010901 DOI: 10.1093/gbe/evw167] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure.
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Affiliation(s)
- Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley Department of Biology, Duke University, Durham
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei
| | | | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley
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21
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A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals. Mol Phylogenet Evol 2016; 98:324-36. [DOI: 10.1016/j.ympev.2016.02.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/15/2016] [Accepted: 02/20/2016] [Indexed: 11/18/2022]
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22
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Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns. Mol Phylogenet Evol 2015; 90:140-9. [DOI: 10.1016/j.ympev.2015.05.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 11/23/2022]
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23
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Eberhard JR, Wright TF. Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 2015; 94:34-46. [PMID: 26291569 DOI: 10.1016/j.ympev.2015.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.
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Affiliation(s)
- Jessica R Eberhard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Timothy F Wright
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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24
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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25
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Rothfels CJ, Johnson AK, Hovenkamp PH, Swofford DL, Roskam HC, Fraser-Jenkins CR, Windham MD, Pryer KM. Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago. Am Nat 2015; 185:433-42. [DOI: 10.1086/679662] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Villarreal JC, Renner SS. A review of molecular-clock calibrations and substitution rates in liverworts, mosses, and hornworts, and a timeframe for a taxonomically cleaned-up genus Nothoceros. Mol Phylogenet Evol 2014; 78:25-35. [DOI: 10.1016/j.ympev.2014.04.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/30/2014] [Accepted: 04/15/2014] [Indexed: 11/16/2022]
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27
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Liu Q, Liu H, Wen J, Peterson PM. Infrageneric phylogeny and temporal divergence of Sorghum (Andropogoneae, Poaceae) based on low-copy nuclear and plastid sequences. PLoS One 2014; 9:e104933. [PMID: 25122516 PMCID: PMC4133246 DOI: 10.1371/journal.pone.0104933] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/12/2014] [Indexed: 01/30/2023] Open
Abstract
The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. x drummondii, S. propinquum, and S. virgatum were closely related to S. x almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (QL); (PMP)
| | - Huan Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Paul M. Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- * E-mail: (QL); (PMP)
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Bellot S, Renner SS. Exploring new dating approaches for parasites: the worldwide Apodanthaceae (Cucurbitales) as an example. Mol Phylogenet Evol 2014; 80:1-10. [PMID: 25057774 DOI: 10.1016/j.ympev.2014.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 11/27/2022]
Abstract
Gene trees of holoparasitic plants usually show distinctly longer branch lengths than seen in photosynthetic closest relatives. Such substitution rate jumps have made it difficult to infer the absolute divergence times of parasites. An additional problem is that parasite clades often lack a fossil record. Using nuclear and mitochondrial DNA sequences of Apodanthaceae, a worldwide family of endoparasites living inside Fabaceae and Salicaceae, we compared several dating approaches: (i) an uncorrelated lognormal (UCLN) model calibrated with outgroup fossils, (ii) ages of host lineages as a maximal age in an UCLN model, (iii) user-assigned local clocks, and (iv) outgroup-fossil-calibrated random local clocks (RLC) with varying prior probabilities on the number of permitted rate changes (RLCu and RLCp models), a variable that has never been explored. The resulting dated phylogenies include all 10 species of the family, three in Australia, one in Iran, one in Africa, and the remainder in the Americas. All clock models infer a drastic rate jump between nonparasitic outgroups and Apodanthaceae, but since they distribute the rate heterogeneity differently, they result in much-different age estimates. Bayes factors using path and stepping-stone sampling indicated that the RLCp model fit poorly, while for matR, topologically unconstrained RLCu and UCLN models did not differ significantly and for 18S, the UCLN model was preferred. Under the equally well fitting models, the Apodanthaceae appear to be a relatively old clade, with a stem age falling between 65 and 81my, the divergence of Apodanthes from Pilostyles between 36 and 57my ago, and the crown age of the Australian clade 8-18my ago. In our study system, host-age calibrations did not yield well-constrained results, but they may work better in other parasite clades. For small data sets where statistical convergence can be reached even with complex models, random local clocks should be explored as an alternative to the exclusive reliance on UCLN clocks.
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Affiliation(s)
- Sidonie Bellot
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
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Zhong B, Fong R, Collins LJ, McLenachan PA, Penny D. Two new fern chloroplasts and decelerated evolution linked to the long generation time in tree ferns. Genome Biol Evol 2014; 6:1166-73. [PMID: 24787621 PMCID: PMC4040995 DOI: 10.1093/gbe/evu087] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report the chloroplast genomes of a tree fern (Dicksonia squarrosa) and a "fern ally" (Tmesipteris elongata), and show that the phylogeny of early land plants is basically as expected, and the estimates of divergence time are largely unaffected after removing the fastest evolving sites. The tree fern shows the major reduction in the rate of evolution, and there has been a major slowdown in the rate of mutation in both families of tree ferns. We suggest that this is related to a generation time effect; if there is a long time period between generations, then this is probably incompatible with a high mutation rate because otherwise nearly every propagule would probably have several lethal mutations. This effect will be especially strong in organisms that have large numbers of cell divisions between generations. This shows the necessity of going beyond phylogeny and integrating its study with other properties of organisms.
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Affiliation(s)
- Bojian Zhong
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Richard Fong
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lesley J Collins
- Faculty of Health Sciences, Universal College of Learning, Palmerston North, New Zealand
| | | | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GKS, Korall P, Pryer KM. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 2013; 8:e76957. [PMID: 24116189 PMCID: PMC3792871 DOI: 10.1371/journal.pone.0076957] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.
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Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Dylan O. Burge
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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