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

Karol et al. BMC Evolutionary Biology 2010, 10:321 http://www.biomedcentral.com/1471-2148/10/321 RESEARCH ARTICLE Open Access Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages Kenneth G Karol1*, Kathiravetpillai Arumuganathan2, Jeffrey L Boore3,4, Aaron M Duffy5, Karin DE Everett6, John D Hall1, S Kellon Hansen5, Jennifer V Kuehl7, Dina F Mandoli6,8, Brent D Mishler9, Richard G Olmstead6, Karen S Renzaglia10, Paul G Wolf5 Abstract 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. Background Patterns and processes of organic evolution are reflected in the structure and sequences of organisms’ genomes. Although we are only starting to accumulate sufficient data to compare nuclear genomes of plants, more data * Correspondence: 1 The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, New York 10458, USA Full list of author information is available at the end of the article are available for the smaller plastid genomes (plastomes). Comparative work on plastomes began in the early 1980’s using restriction site mapping and hybridization with heterologous probes to generate phylogenetically informative data within small clades, generally below the family level [1,2] as well as using comparative mapping to examine differences among more distantly related groups [3-6]. By the 1990’s the emphasis shifted to nucleotide sequences from targeted regions (genes) © 2010 Karol et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Karol et al. BMC Evolutionary Biology 2010, 10:321 http://www.biomedcentral.com/1471-2148/10/321 with the result that studies with broad genomic sampling were few. However, a reduction in sequencing cost and concomitant development of analytical tools over the past 10 years has resulted in resurgence of comparative plastid genomics. The plastome is highly conserved in overall structure and this provides the basis for comparative studies [4]. However, there is still sufficient variation to identify rare genomic events that mark critical branches in land plant evolution, thereby elucidating early evolutionary modifications to the plastid genome [e.g., [5,7]]. Plastomes of Marchantia polymorpha [8] and Nicotiana tabacum [9] were the first to be sequenced and within 19 years there were 45 complete plastome sequences for green plants (Viridiplantae) in GenBank [10]. Acceleration of efforts yielded 146 plastome sequences by the end of 2009, with many others in progress. Complete genome sequences offer several advantages over restriction site maps and nucleotide sequences of targeted regions. In addition to substantially increasing the number of gene sequences for comparison, plastome sequences provide vast structural and evolutionary information that includes gene order, genome rearrangements, patterns of base pair composition, codon usage, mechanisms of gene duplication and gene loss (e.g., pseudogenization), patterns of nucleotide insertion and deletion (indels), and the occurrence of noncoding regions (such as plastome microsatellites and introns). We now have sufficient sampling from most major land plant clades to begin comparative analyses of their plastomes in earnest. Despite considerable progress over the last 15 years in our understanding of green plant phylogeny, several nodes remain poorly resolved. One example is the monilophytes, which include five major lineages: leptosporangiate ferns, horsetails, marattioid ferns, ophioglossoid ferns and psilophytes. The monilophytes seem to be well-supported as a group, and are generally accepted as sister to seed plants [11-14]. But relationships among the major monilophyte lineages remain unclear. Here we present the complete plastome for the horsetail Equisetum arvense L., representing one of the last major monilophyte lineages to have a representative complete plastome available. For further resolution of land plant relationships and plastome evolution we also sequenced the plastome of Isoetes flaccida Shuttlw. ex A. Braun, the last of the three major lycophyte lineages to be sampled. We use data for 49 genes from 43 green plant taxa to infer phylogenetic relationships of land plants and compile information on the distribution of gene translocations, genomic inversions, gene content and indels to augment the phylogenetic signal from gene variation. We also examine codon usage and base composition. Patterns of plastome architecture are compared Page 2 of 16 across early land plant lineages that diverged 400 to 500 million years ago. Results and Discussion Our analyses included representatives of all major land plant lineages as well as sampling of charophycean green algae for appro (...truncated)