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Full Plastome Sequence of the Fern Vandenboschia Speciosa (Hymenophyllales): Structural Singularities and Evolutionary Insights

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Full Plastome Sequence of the Fern Vandenboschia Speciosa (Hymenophyllales): Structural Singularities and Evolutionary Insights Journal of Plant Research https://doi.org/10.1007/s10265-018-1077-y REGULAR PAPER Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights F. J. Ruiz‑Ruano1 · B. Navarro‑Domínguez1 · J. P. M. Camacho1 · Manuel A. Garrido‑Ramos1 Received: 9 July 2018 / Accepted: 26 November 2018 © The Botanical Society of Japan and Springer Japan KK, part of Springer Nature 2018 Abstract We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the diversity of plastomes throughout fern evolution. Gene content of V. speciosa plastome was similar to that in most ferns, although there were some characteristic gene losses and lineage-specific differences. In addition, an important number of genes required U to C RNA editing for proper protein translation and two genes showed start codons alternative to the canonical AUG (AUA). Concern- ing gene order, V. speciosa shared the specific 30-kb inversion of euphyllophytes plastomes and the 3.3-kb inversion of fern plastomes, keeping the ancestral gene order shared by eusporangiate and early leptosporangiate ferns. Conversely, V. speciosa has expanded IR regions comprising the rps7, rps12, ndhB and trnL genes in addition to rRNA and other tRNA genes, a condition shared with several eusporangiate ferns, lycophytes and hornworts, as well as most seed plants. Keywords Ferns · Gene losses · IR expansion · Non-canonical start codons · Plastome · RNA editing · Vandenboschia speciosa Introduction composed of genes related with their function in the eukary- otic cell, so that the plastome contains genes that encode The era of genomics allows not only the untangling of the for proteins involved in photosynthesis and for proteins and most recondite details of nuclear genome composition in RNAs involved in gene expression. eukaryotic cells, but also facilitates the study of the genomes Plastomes of land plants are generally conserved in struc- of cytoplasmic organelles in a relatively simple and time- ture, gene content and gene order (Gao et al. 2010; Green saving way. Eukaryotic cells contain mitochondria respon- 2011; Ruhlman and Jansen 2014; Wicke et al. 2011; Wolf sible for cellular respiration and cellular metabolism regu- et al. 2010; Wolf and Karol 2012; Xu et al. 2015). Most lation. Specifically, plants are characterized by also having plastomes are characterized by a quadripartite structure, chloroplasts that allow plants to convert light energy into including two copies of an inverted repeat (IRA and IRB) chemical energy through photosynthesis. Both organelles and the large (LSC), and small (SSC) single copy regions. are prokaryotic endosymbionts in origin and both contain The plastome usually includes 120–130 genes and varies in their own genomes, which have been drastically reduced size from 120 to 170 kilobases (kb). However, specific line- during evolution. Current organelle genomes are basically ages of land plants are characterized by gene and/or intron losses or duplications changing gene content in the plastome as well as some rearrangements changing its gene order Electronic supplementary material The online version of this (Gao et al. 2010; Green 2011; Ruhlman and Jansen 2014; article (https ://doi.org/10.1007/s1026 5-018-1077-y) contains Wicke et al. 2011; Wolf et al. 2010; Wolf and Karol 2012; supplementary material, which is available to authorized users. Xu et al. 2015). These changes appear to be phylogenetically * Manuel A. Garrido-Ramos informative (Gao et al. 2009, 2011, 2013; Grewe et al. 2013; [email protected] Karol et al. 2010; Kim et al. 2014; Logacheva et al. 2017; Wolf et al. 2010; Zhu et al. 2016) and some examples are 1 Departamento de Genética, Facultad de Ciencias, known in bryophytes (e.g. Park et al. 2018; Wolf and Karol Universidad de Granada, Granada, Spain Vol.:(0123456789)1 3 Journal of Plant Research 2012), lycophytes (e.g. Guo et al. 2016; Tsuji et al. 2007; Wolf et al. 2005), monilophytes (e.g., Gao et al. 2009, 2011, 2013; Grewe et al. 2013; Karol et al. 2010; Kim et al. 2014; Logacheva et al. 2017; Lu et al. 2015; Roper et al. 2007; Wolf et al. 2003, 2010; Zhong et al. 2014; Zhu et al. 2016), and seed plants (in both gymnosperm and angiosperm line- ages) (e.g. Green 2011; Ruhlman and Jansen 2014; Sun et al. 2016; Wicke et al. 2011; Xu et al. 2015; Zhu et al. 2016). Plastome sequence is thus a useful tool to build phylog- enies which have contributed very much to our understand- ing of plant evolution. It is thus essential to analyze plastome diversity across all plant lineages, and this is especially cru- cial in understudied groups such as ferns (Gao et al. 2013; Grewe et al. 2013; Karol et al. 2010; Kim et al. 2014; Labiak and Karol 2017; Roper et al. 2007; Wolf et al. 2010). Extant ferns are a lineage of non-seed vascular plants including 45 families and about 280 genera (Knie et al. 2015; Lehtonen 2011, PPG I 2016; Qi et al. 2018; Rai and Graham 2010; Rothfels et al. 2015; Schuettpelz and Pryer 2007). Molecu- lar phylogenies have revealed a basal dichotomy within the vascular plants (Pryer et al. 2001), separating the lyco- phytes (less than 1% of the current vascular plants) from the euphilophytes, among which there are two major clades, Fig. 1 Schematic representation of currently accepted ordinal fern the monilophytes or ferns and the spermatophytes or seed phylogeny (PPG I 2016) derived from the best available data (mainly from Knie et al. 2015; Lehtonen 2011; Qi et al. 2018; Rai and Gra- plants. Monilophyte includes the classes Psilotopsida (orders ham 2010; Rothfels et al. 2015; Schuettpelz and Pryer 2007) Psilotales and Ophioglossales), Equisetopsida (order Equi- setales), Marattiopsida (order Marattiales) and Polypodi- opsida (Fig. 1). The class Polypodiopsida, also known as (Lu et al. 2015). This clearly indicates that the diversity of leptosporangiate ferns (sporangia arise from a single epi- plastome structures in ferns has insufficiently been explored, dermal cell and not from a group of cells as in eusporangi- precluding a comprehensive study of plastome evolution ate ferns), includes the vast majority of extant ferns, with in this group (Grewe et al. 2013; Logacheva et al. 2017). more than 80% of about 10,500 fern species. Conversely, Furthermore, among complete plastome sequences, there the classes Psilotopsida, Equisetopsida and Marattiopsida are no representatives from the order Hymenophyllales, comprise the grade of eusporangiate ferns. The monophy- a key lineage within non-core, early leptosporangiates. letic group of leptosporangiates is composed of a total of Thus, the recent phyloplastomic analysis of ferns carried seven orders (Knie et al. 2015; Lehtonen 2011, PPG I 2016; out by Lu et al. (2015) included at least one representa- Qi et al. 2018; Rai and Graham 2010; Rothfels et al. 2015; tive species of each Monilophyte order except for the order Schuettpelz and Pryer 2007). Three leptosporangiate orders, Hymenophyllales. Salviniales (heterosporous ferns), Cyatheales (tree ferns), Our aim here is to fill this gap by analyzing the full and Polypodiales (polypods), form the large monophyletic sequence of the plastome of Vandenboschia speciosa clade of core leptosporangiates (Smith et al. 2006). The rest (Hymenophyllaceae, Hymenophyllales). The family Hyme- of leptosporangiate species are included within the orders nophyllaceae, with about 600 species, has its origin in the Osmundales, Hymenophyllales, Gleicheniales and Schizae- Triassic and its highest degree of diversification took place ales (Fig. 1). about 160 mya during the Jurassic (Pryer et al. 2004). This Among the nearly 2,000 complete plastome sequences family is characterized by the “filmy” aspect of its sporo- available in the GenBank database, only less than 50 belong phytes (fronds constituted by a translucent sheet with a sin- to monilophytes (Kim et al. 2014; Logacheva et al. 2017; Lu gle layer of cells). Although this family shows pantropical et al. 2015; Zhu et al. 2016; our own look-over to the NCBI distribution, with high diversity in morphology and habitat web page https ://www.ncbi.nlm.nih.gov/genom e/brows e#!/ occupation (Dubuisson et al. 2003; Ebihara et al. 2007), V. organ elles /). In addition, the information about fern plasto- speciosa constitutes a rare Macaronesian-European end- mes is limited to a few representatives of most, but not all, emism, as it is the only representative in the area and one fern orders. And, within the different orders, only a few rep- of the most vulnerable fern species in Europe, restricted to resentative species have been analyzed from some families places considered as refuges of tertiary flora. The two phases 1 3 Journal of Plant Research of its life cycle are perennial and capable of reproducing by of this sequence with other plant plastomes performing a vegetative propagation (Rumsey et al. 1999). The sporophyte BLASTN (Altschul et al. 1990) search against the NCBI’s is rhizomatous and able to spread by fragmentation of its NR database. Once homology was confirmed with plasto- rhizome. The gametophyte is very different from the typi- mes, we used this partial sequence as a seed to assembly cal heart-shaped prothallus, it is characterized by being epi- the remaining sequence of the V. speciosa plastome using a geous and narrowly talose or filamentous (to such an extent random selection of 2 × 2,000,000 reads with the MITObim that it is often confused with the protonema of a bryophyte), v1.8 software (Hahn et al. 2013) with the “—quick” option. and produces geminiferous buds. All these characteristics A single run of MITObim was unable to assembly the full add valuable scientific interest to the selection of this species sequence, for which reason we used the assembled sequence as representative of the order Hymenophyllales for plastome for a new run with this same software in order to lengthen sequencing.
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