The evolution of chloroplast genes and genomes in ferns

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.     

Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of co-dons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.     

石松类和蕨类植物质体基因组结构演化研究进展

近年来, 随着测序技术的发展, 石松类和蕨类植物的核基因组、质体基因组以及线粒体基因组研究发展迅速, 质体基因组研究工作更是呈爆发式增长。截至2019年3月1日, GenBank公布的石松类和蕨类植物的175个质体基因组中, 约3/4为最近两年新增。研究内容从早期对个别质体基因组结构和序列特征的简单报道, 逐渐发展到综合性的比较基因组学和系统发育基因组学研究。目前已发表的质体基因组覆盖了石松类和蕨类植物的所有目和大部分科, 这两大类群的质体基因组结构变异和系统发育的基本框架已逐渐清晰。这些研究为我们理解维管植物的早期演化提供了重要参考。本文对石松类和蕨类植物的质体基因组结构特征进行了系统梳理, 发现其结构变异主要包括大片段倒位、IR区边界变动、基因或内含子丢失等, 其中一些结构变异可作为较高分类阶元的共衍征。RNA编辑和长片段非编码序列插入普遍存在于石松类和蕨类植物的质体基因组中, 但其起源、演化机制和功能等仍不清楚。我们对质体基因组的应用、系统发育研究中质体和核基因组的优劣性, 以及系统发育基因组学的前景进行了评述。     

Spatial genetic analyses reveal strong genetic structure in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae)

The development of spatial genetic structure (SGS) in seed plants has been linked to several biological attributes of species, such as breeding system and life form. However, little is known about SGS in ferns, which together with lycopods are unique among land plants in having two free‐living life stages. We combined spatial aggregation statistics and spatial genetic autocorrelation analyses using five plastid microsatellites and one nuclear gene to investigate SGS in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae). We assessed how the observed patterns compare with those estimated for other ferns and seed plants. Populations of A. firma exhibited strong SGS, spatial clustering of individuals, substantial clonal diversity and no inbreeding. SGS in ferns appears to be higher than in most seed plants analysed to date. Contrary to our expectations, an outcrossing breeding system, wind dispersal and an arborescent life form did not translate into weak or no SGS. In ferns, SGS is probably being affected by the life cycle with two free‐living life stages. The reproductive biology of ferns appears to be more complex than previously thought. This implies that SGS in ferns is affected by some factors that cannot be inferred from the study of flowering plants. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 439–449.     

Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences

Abstract: A conserved coding region of the mitochondrial nad5 gene (1098–1107 bp of protein coding sequence) was amplified from 30 pteridophytes (26 ferns and 4 fern allies). A group II intron sequence conserved in all ferns except the eu-sporangiate genus Ophioglossum is also present in the whisk fern Psilotum nudum and the lycopod Huperzia selogo , but absent from the horsetails ( Equisetum ), the seed plants and the bryo-phytes. Phylogenetic trees constructed with different methods consistently suggest several monophyletic units. The conserved group II intron sequence provides valuable additional phylogenetic information. Leptosporangiate ferns are monophyletic with Osmunda as the basal-most branching genus followed by Trichomanes, Matonia and Lygodium . These genera are set distantly apart from other leptosporangiate ferns, including the tree and water ferns, which branch in close proximity. Species of Polypodiaceae, Dryopteridaceae, Thelypteridaceae, Aspleniaceae and Blechnaceae appear in a monophyletic crown group of derived leptosporangiate ferns with Dryopteridaceae as a paraphyletic taxon. Placement of Psilotum in a class of its own receives no support from the mitochondrial sequences, which rather suggest its inclusion among eusporangiate ferns (Ophioglossales). RNA editing is required to correct the genetic information of the nad5 gene in all species investigated and includes the removal of stop codons from the reading frames. The influence of RNA editing on phylogenetic tree construction is investigated and discussed.     

Tomato contains homologues of Arabidopsis cryptochromes 1 and 2

Cryptochromes are blue light photoreceptors found in both plants and animals. They probably evolved from photolyases, which are blue/UV-light-absorbing photoreceptors involved in DNA repair. In seed plants, two different cryptochrome (CRY) genes have been found in Arabidopsis and one in Sinapis, while three genes have been found in the fern Adiantum. We report the characterisation of tomato CRY genes CRY1 and CRY2. They map to chromosomes 4 and 9, respectively, show relatively constitutive expression and encode proteins of 679 and 635 amino acids, respectively. These proteins show higher similarity to their Arabidopsis counterparts than to each other, suggesting that duplication between CRY1 and CRY2 is an ancient event in the evolution of seed plants. The seed plant cryptochromes form a group distinct from the fern cryptochromes, implying that only one gene was present in the common ancestor between these two groups of plants. Most intron positions in CRY genes from plants and ferns are highly conserved. Tomato cry1 and cry2 proteins carry C-terminal domains 210 and 160 amino acids long, respectively. Several conserved motifs are found in these domains, some of which are common to both types of cryptochromes, while others are cryptochrome-type-specific.     

蕨类植物的化感作用及其对生物多样性的影响

植物化感作用是植物通过向环境中释放化学物质从而对同种植株和繁殖体或与其他植物之间产生的直接或间接、有益或有害的作用,它影响植物分布、群落形成与演化、作物间作等,与生物多样性保护以及农林和园艺生产实践关系密切,在国际上受到越来越多的关注。但国内这方面的研究起步相对较晚,研究范围有限,对蕨类植物化感作用的报道更少。本文系统介绍了蕨类植物化感作用的研究进展,包括蕨类植物种内的化感作用(即自毒效应)、常见的蕨类植物种间的化感作用(即孢子体对配子体的化感作用和配子体对配子体的化感作用)及蕨类植物对种子植物的化感作用(蕨类植物可通过化感作用与种子植物争夺更多的资源和生长空间)。还介绍了种子植物对蕨类植物的化感作用(主要表现为抑制作用)以及蕨类植物化感作用与动物侵食、微生物侵染的关系,研究发现昆虫侵食能增强或减弱蕨类植物的化感作用,微生物的活动可能增强某些蕨类植物的化感作用。本文从上述不同角度说明蕨类植物化感作用对生物多样性的影响,希望有助于促进我国学者对该领域的深入研究。     

Contrasting Predictors of Fern versus Angiosperm Decomposition in a Common Garden

We evaluated differences in the rates and correlates of decomposition among 32 fern and angiosperm litter types collected in Hawai'i. Leptosporangiate ferns were separated into groups based on phylogeny: 'polypod' ferns, a monophyletic clade of ferns that diversified in the Cretaceous, and all other ('non-polypod') ferns that diversified earlier. We measured initial litter chemistry (nutrients and carbon chemistry), and mass loss and nitrogen (N), phosphorus (P), and calcium (Ca) of litter tissue during a 1-yr incubation in a common garden. Nutrient concentrations and carbon (C) chemistry differed significantly among litter types, and litter turnover ( k -values) ranged from 0.29 to 8.31. Decomposition rates were more closely correlated with nutrient concentration than is typically observed. Lignin:N was the best predictor of decomposition across all litter types combined; however, among plant groups different predictors of decomposition were important. Nitrogen and P concentrations best predicted fern decomposition, whereas C chemistry, particularly lignin concentration, was more important for angiosperm (monocot and dicot) decomposition. Among native plants, non-polypod ferns decomposed significantly more slowly than both polypod ferns and angiosperms. Contrary to our hypothesis, fern litter did not decompose more slowly than angiosperm litter overall. Nutrient dynamics in litter were affected by initial litter concentration more than phylogeny; low-nutrient litter immobilized more nutrients than high-nutrient litter. Systematic differences in rates of decomposition, and the importance of nutrients in predicting fern decomposition, imply that changes in species composition within ferns and between ferns and angiosperms could influence the functioning of ecosystems where ferns are important forest components.     

The invention of WUS-like stem cell-promoting functions in plants predates leptosporangiate ferns

The growth of land plants depends on stem cell-containing meristems which show major differences in their architecture from basal to higher plant species. In Arabidopsis, the stem cell niches in the shoot and root meristems are promoted by WUSCHEL (WUS) and WOX5, respectively. Both genes are members of a non-ancestral clade of the WUS-related homeobox (WOX) gene family, which is absent in extant bryophytes and lycophytes. Our analyses of five fern species suggest that a single WUS orthologue was present in the last common ancestor (LCA) of leptosporangiate ferns and seed plants. In the extant fern Ceratopteris richardii, the WUS pro-orthologue marks the pluripotent cell fate of immediate descendants of the root apical initial, so-called merophytes, which undergo a series of stereotypic cell divisions and give rise to all cell types of the root except the root cap. The invention of a WUS-like function within the WOX gene family in an ancestor of leptosporangiate ferns and seed plants and its amplification and sub-functionalisation to different stem cell niches might relate to the success of seed plants, especially angiosperms.     

Ancestry of plant MADS-box genes revealed by bryophyte (Physcomitrella patens) homologues

Three MADS-box cDNA clones and two corresponding genomic sequences (gDNAs) have been isolated from the bryophyte Physcomitrella patens and sequenced. Our findings indicate that the genes may be expressed in a tissue- or age-specific manner, and that expression of one of them is regulated by an alternative splicing mechanism. Conceptual translation of the clones reveals that the encoded MADS-domain proteins have the typical plant-domain pattern (MIKC). Additionally, there is a high degree of conservation of intron number and positions between angiosperm MADS-box genes and the moss loci. These observations confirm the homology of moss and higher plant MADS-box genes. We conclude that the MIKC pattern evolved in MADS-box genes after the separation of the plant lineage from that of fungi and animals, and that it must have been present in the common ancestor of mosses, ferns and seed plants. Therefore it evolved at least 400 million yr ago. Phylogenetic analysis of a large subset of the sequenced plant MADS-box genes, incorporating those from P. patens , indicates that the bryophyte genes are not orthologues of spermatophyte genes belonging to any of the well recognized higher plant gene subfamilies. This conclusion accords well with reports that the known fern MADS-box genes also comprise subfamilies distinct from those of higher plants. Therefore we tentatively propose that the gene duplication and diversification events that created the MADS-box gene subfamilies, discernible in extant angiosperm and other spermatophyte groups, occurred after separation of the moss and fern lineages from the lineage which produced the higher plants.     

First insights into fern matK phylogeny

MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.     

Stomatal morphology and physiology explain varied sensitivity to abscisic acid across vascular plant lineages

Abscisic acid (ABA) can induce rapid stomatal closure in seed plants, but the action of this hormone on the stomata of fern and lycophyte species remains equivocal. Here, ABA-induced stomatal closure, signaling components, guard cell K⁺ and Ca²⁺ fluxes, vacuolar and actin cytoskeleton dynamics, and the permeability coefficient of guard cell protoplasts (P_f) were analyzed in species spanning the diversity of vascular land plants including 11 seed plants, 6 ferns, and 1 lycophyte. We found that all 11 seed plants exhibited ABA-induced stomatal closure, but the fern and lycophyte species did not. ABA-induced hydrogen peroxide elevation was observed in all species, but the signaling pathway downstream of nitric oxide production, including ion channel activation, was only observed in seed plants. In the angiosperm faba bean (Vicia faba), ABA application caused large vacuolar compartments to disaggregate, actin filaments to disintegrate into short fragments and P_f to increase. None of these changes was observed in the guard cells of the fern Matteuccia struthiopteris and lycophyte Selaginella moellendorffii treated with ABA, but a hypertonic osmotic solution did induce stomatal closure in fern and the lycophyte. Our results suggest that there is a major difference in the regulation of stomata between the fern and lycophyte plants and the seed plants. Importantly, these findings have uncovered the physiological and biophysical mechanisms that may have been responsible for the evolution of a stomatal response to ABA in the earliest seed plants.

Physiological and biophysical evidence for insensitivity of stomata to abscisic acid in ferns and lycophytes supports stomatal responsiveness to abscisic acid evolved after the divergence of ferns.     

海南和台湾蕨类植物多样性及其大陆性特征

海南和台湾是我国南部和东部两个最重要的大陆性岛屿,具有极为丰富的蕨类植物多样性。特有现象揭示着植物区系和植物多样性的历史,间断分布揭示着与邻近或相关植物区系的联系;特别是在岛屿地区,这种现象和意义尤其明显。海南有蕨类植物区系55科、135属、466种,其中特有种有32种,台湾蕨类植物区系57科、142属、599种,其中特有种达66种。在海南与台湾两地,有共有属104属,共有种仅有176种。台湾海峡出现始于晚白垩世,持续至第四纪;琼州海峡出现于早第四纪,因此,两地的特有现象远少于种子植物(台湾有801种,海南有501种),原因与蕨类植物具有更广的散布性相关,而且在被子植物中起重要作用的物种生物学障碍(机制)在蕨类是缺乏的;形态学的、生殖生物学特征导致蕨类植物具有较缓慢的物种演化历史和较低的灭绝率(Smith,1972)。海南和台湾蕨类植物区系的比较还表明,地理位置和海拔高度对植物区系的物种分化和物种多样性产生了极大的影响。     

Stomatal innovation and the rise of seed plants

Stomatal valves on the leaves of vascular plants not only prevent desiccation but also dynamically regulate water loss to maintain efficient daytime water use. This latter process involves sophisticated active control of stomatal aperture that may be absent from early-branching plant clades. To test this hypothesis, we compare the stomatal response to light intensity in 13 species of ferns and lycophytes with a diverse sample of seed plants to determine whether the capacity to optimise water use is an ancestral or derived feature of stomatal physiology. We found that in seed plants, the ratio of photosynthesis to water use remained high and constant at different light intensities, but fern and lycophyte stomata were incapable of sustaining homeostatic water use efficiency. We conclude that efficient water use in early seed plants provided them with a competitive advantage that contributed to the decline of fern and lycophyte dominated-ecosystems in the late Paleozoic.     

KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems

Members of the class 1 knotted-like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.     

Chloroplast phylogenomics resolves key relationships in ferns

Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae(Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales–Ophioglossales clade, and Equisetales–Psilotales–Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae–eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.     

Passiflora plastome sequencing reveals widespread genomic rearrangements

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.     

Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails

Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies already has provided critical insight into some long-standing questions about the evolution of land plants. Here we report on the presence of a group II intron located in the mitochondrial atp1 gene of leptosporangiate and marattioid ferns. Primary sequence data for the atp1 gene are newly reported for 27 taxa, and results are presented from maximum likelihood-based phylogenetic analyses using Bayesian inference for 34 land plants in three data sets: (1) single-gene mitochondrial atp1 (exon+intron sequences); (2) five combined genes (mitochondrial atp1 [exon only]; plastid rbcL, atpB, rps4; nuclear SSU rDNA); and (3) same five combined genes plus morphology. All our phylogenetic analyses corroborate results from previous fern studies that used plastid and nuclear sequence data: the monophyly of euphyllophytes, as well as of monilophytes; whisk ferns (Psilotidae) sister to ophioglossoid ferns (Ophioglossidae); horsetails (Equisetopsida) sister to marattioid ferns (Marattiidae), which together are sister to the monophyletic leptosporangiate ferns. In contrast to the results from the primary sequence data, the genomic structural data (atp1 intron distribution pattern) would seem to suggest that leptosporangiate and marattioid ferns are monophyletic, and together they are the sister group to horsetails--a topology that is rarely reconstructed using primary sequence data.     

Genetic and genomic aspects of hybridization in ferns

The morphological and ecological intermediacy of hybrid taxa has long interested and challenged fern biologists, resulting in numerous systematic contributions focused on disentangling relationships within reticulate species complexes. From a genetic perspective, hybrid ferns are especially interesting because they represent the union of divergent parental genomes in unique evolutionary entities. This review summarizes advances in our knowledge of the genetic and genomic aspects of hybridization in ferns from the mid-20th century to the present. The different organismal products of hybridization, evolutionary aspects of additive and non-additive gene expression in allopolyploids, genetic and genomic mechanisms leading to gene silencing and loss, the roles of multiple origins and introgression for imparting genetic variation to hybrid fern taxa and their progenitors, and the utility of allopolyploid ferns to investigate mechanisms of genome evolution in the homosporous ferns are discussed. Comparisons are made to other plant lineages and important future research directions are highlighted, with the goal of stimulating additional research on hybrid ferns.