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Title: Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Journal Article · · BMC Evolutionary Biology (Online)
 [1];  [2];  [3];  [4];  [5];  [6];  [4];  [7];  [5];  [8];  [5];  [9];  [4]
  1. The New York Botanical Garden, Bronx, NY (United States). The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies; DOE/OSTI
  2. Benaroya Research Inst. at Virginia Mason, Seattle, WA (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Geonome Project Solutions, Hercules, CA (United States)
  4. Utah State Univ., Logan, UT (United States). Dept. of Biology. Ecology Center
  5. Univ. of Washington, Seattle, WA (United States). Dept. of Biology
  6. The New York Botanical Garden, Bronx, NY (United States). The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
  8. Univ. of California, Berkeley, CA (United States). Dept. of Integrative Biology
  9. Southern Illinois Univ., Carbondale, IL (United States). Plant Biology--SIUC
+ Show Author Affiliations

Background: Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats. Results: We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes. Conclusions: Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the “true ferns,” including Marattiaceae.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1626370
Journal Information:
BMC Evolutionary Biology (Online), Journal Name: BMC Evolutionary Biology (Online) Journal Issue: 1 Vol. 10; ISSN 1471-2148
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions journal January 2014
The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae journal April 2018
The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske journal March 2018
Evolutionary Morphology of Ferns (Monilophytes) book January 2012
Evolutionary Morphology of Ferns (Monilophytes) book April 2018
Origin of Equisetum : Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida journal July 2018
Order-level fern plastome phylogenomics: new insights from Hymenophyllales journal August 2018
Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution journal December 2019
The evolution of chloroplast genes and genomes in ferns journal October 2010
The evolution of the plastid chromosome in land plants: gene content, gene order, gene function journal March 2011
Genetic relationships and ecological divergence in Salix species and populations in Taiwan journal April 2015
Biology and Functional Ecology of Equisetum with Emphasis on the Giant Horsetails journal January 2013
Phylotranscriptomic analysis of the origin and early diversification of land plants journal October 2014
Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies journal May 2018
The complete chloroplast genome of Isoetes yunguiensis (Isoetaceae), a rare and endangered fern endemic to China journal January 2019
Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads journal January 2013
Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants journal March 2014
Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content journal July 2016
Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity journal June 2017
Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids journal September 2017
The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR-Coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte) journal April 2019
Transcriptomic Evidence for the Evolution of Shoot Meristem Function in Sporophyte-Dominant Land Plants through Concerted Selection of Ancestral Gametophytic and Sporophytic Genetic Programs journal November 2014
Transcriptomic Evidence for the Evolution of Shoot Meristem Function in Sporophyte-Dominant Land Plants through Concerted Selection of Ancestral Gametophytic and Sporophytic Genetic Programs journal September 2015
Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions journal January 2014
Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias journal July 2014
Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants journal November 2019
The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) ‘On the plant-remains from the Downtonian of England and Wales' journal April 2015
Phylogenomics supports a Cenozoic rediversification of the “living fossil” Isoetes posted_content December 2019
Phylogenomics and barcoding of Panax: toward the identification of ginseng species posted_content January 2018
Phylogenetic conflicts, combinability, and deep phylogenomics in plants posted_content October 2019
Chloroplast phylogenomics resolves key relationships in ferns: Chloroplast phylogenomics in ferns journal September 2015
The complete plastid genome sequence of Trichomanes trollii (Hymenophyllaceae) journal December 2018
Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.) journal December 2018
Lycophyte plastid genomics: extreme variation in GC , gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat journal January 2019
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes journal January 2014
Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns – a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles journal June 2016
Phylogenomics and barcoding of Panax: toward the identification of ginseng species journal April 2018
Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida) journal June 2019
Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns journal October 2013
The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae journal April 2018
Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae journal August 2018
The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske journal March 2018

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