Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

BACKGROUND

Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae.

RESULTS

The chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae.

CONCLUSIONS

Our study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.

Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

BACKGROUND

Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes.

RESULTS

We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a "ghost lineage," and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae.

CONCLUSIONS

This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate (Punica granatum L.)

Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, “1201” and “1181”) to 158,662 bp (cultivar, “Gul-e-Shah Red”) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (“Helow,” “Tunisia,” and “Bhagawa”), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164–165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].

A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.

Implications of plastome evolution in the true lilies (monocot order Liliales)

The families of the monocot order Liliales exhibit highly contrasting characteristic of photosynthetic and mycoheterotrophic life histories. Although previous phylogenetic and morphological studies of Liliales have been conducted, they have not examined molecular evolution associated with this contrasting phenomenon. Here, we conduct the first comparative plastome study of all ten families of Liliales using 29 newly sequenced plastid genomes analyzed together with previously published data. We also present a phylogenetic analysis for Liliales of 78 plastid genes combined with 22 genes from all three genomes (nuclear 18S rDNA and phyC; 17 plastid genes; and mitochondrial matR, atpA, and cob). Within the newly generated phylogenetic tree of Liliales, we evaluate the ancestral state changes of selected morphological traits in the order. There are no significant differences in plastid genome features among species that show divergent characteristics correlated with family circumscriptions. However, the results clearly differentiate between photosynthetic and mycoheterotrophic taxa of Liliales in terms of genome structure, and gene content and order. The newly sequenced plastid genomes and combined three-genome data revealed Smilacaceae as sister to Liliaceae instead of Philesiaceae and Ripogonaceae. Additionally, we propose a revised familial classification system of Liliales that consists of nine families, considering Ripogonaceae a synonym of Philesiaceae. The ancestral state reconstruction indicated synapomorphies for each family of Liliales, except Liliaceae, Melanthiaceae and Colchicaceae. A taxonomic key for all nine families of Liliales is also provided.

A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree

A novel test is described that visualizes the absolute model-data fit of the substitution and tree components of an evolutionary model. The test utilizes statistics based on counts of character state matches and mismatches in alignments of observed and simulated sequences. This comparison is used to assess model-data fit. In simulations conducted to evaluate the performance of the test, the test estimator was able to identify both the correct tree topology and substitution model under conditions where the Goldman-Cox test-which tests the fit of a substitution model to sequence data and is also based on comparing simulated replicates with observed data-showed high error rates. The novel test was found to identify the correct tree topology within a wide range of DNA substitution model misspecifications, indicating the high discriminatory power of the test. Use of this test provides a practical approach for assessing absolute model-data fit when testing phylogenetic hypotheses.

Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.

Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)

In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.

Accelerated Estimation of Frequency Classes in Site-Heterogeneous Profile Mixture Models

As a consequence of structural and functional constraints, proteins tend to have site-specific preferences for particular amino acids. Failing to adjust for heterogeneity of frequencies over sites can lead to artifacts in phylogenetic estimation. Site-heterogeneous mixture-models have been developed to address this problem. However, due to prohibitive computational times, maximum likelihood implementations utilize fixed component frequency vectors inferred from sequences in a database that are external to the alignment under analysis. Here, we propose a composite likelihood approach to estimation of component frequencies for a mixture model that directly uses the data from the alignment of interest. In the common case that the number of taxa under study is not large, several adjustments to the default composite likelihood are shown to be necessary. In simulations, the approach is shown to provide large improvements over hierarchical clustering. For empirical data, substantial improvements in likelihoods are found over mixtures using fixed components.

Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids

The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.

Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae

Chloroplast genomes of plants are highly conserved in both gene order and gene content, are maternally inherited, and have a lower rate of evolution. Chloroplast genomes are considered to be good models for testing lineage-specific molecular evolution. In this study, we use Schisandraceae as an example to generate insights into the overall evolutionary dynamics in chloroplast genomes and to establish the phylogenetic relationship of Schisandraceae based on chloroplast genome data using phylogenomic analysis. By comparing three Schisandraceae chloroplast genomes, we demonstrate that the gene order, gene content, and length of chloroplast genomes in Schisandraceae are highly conserved but experience dynamic evolution among species. The number of repeat variations were detected, and the Schisandraceae chloroplast genome was revealed as unusual in having a 10 kb contraction of the IR due to the genome size variations compared with other angiosperms. Phylogenomic analysis based on 82 protein-coding genes from 66 plant taxa clearly elucidated that Schisandraceae is a sister to a clade that includes magnoliids, monocots, and eudicots within angiosperms. As to genus relationships within Schisandraceae, Kadsura and Schisandra formed a monophyletic clade which was sister to Illicium.

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale

The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution

Background

The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies.

Results

All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859–26,451 bp) separated by a large single-copy region (86,089–87,835 bp) and a small single-copy region (18,250–18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified.

Conclusions

Phylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4319-9) contains supplementary material, which is available to authorized users.

Complete Chloroplast Genome Sequence of Decaisnea insignis: Genome Organization, Genomic Resources and Comparative Analysis

Decaisnea insignis is a wild resource plant and is used as an ornamental, medicinal, and fruit plant. High-throughput sequencing of chloroplast genomes has provided insight into the overall evolutionary dynamics of chloroplast genomes and has enhanced our understanding of the evolutionary relationships within plant families. In the present study, we sequenced the complete chloroplast genome of D. insignis and used the data to assess its genomic resources. The D. insignis chloroplast genome is 158,683 bp in length and includes a pair of inverted repeats of 26,167 bp that are separated by small and large single copy regions of 19,162 bp and 87,187 bp, respectively. We identified 83 simple sequence repeats and 18 pairs of large repeats. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited a high A/T content. The D. insignis chloroplast genome bias was skewed towards A/T on the basis of codon usage. A phylogenetic tree based on 82 protein-coding genes of 33 angiosperms showed that D. insignis was clustered with Akebia in Lardizabalaceae. Overall, the results of this study will contribute to better understanding the evolution, molecular biology and genetic improvement of D. insignis.

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)

Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.

Taxonomic description of in situ bee pollen from the middle Eocene of Germany

The middle Eocene Messel and Eckfeld localities are renowned for their excellently preserved faunas and diverse floras. Here we describe for the first time pollen from insect-pollinated plants found in situ on well-preserved ancient bees using light and scanning electron microscopy. There have been 140 pollen types reported from Messel and 162 pollen types from Eckfeld. Here we document 23 pollen types, six from Messel and 18 from Eckfeld (one is shared). The taxa reported here are all pollinated by insects and mostly not recovered in the previously studied dispersed fossil pollen records. Typically, a single or two pollen types are found on each fossil bee specimen, the maximum number of distinct pollen types on a single individual is five. Only five of the 23 pollen types obtained are angiosperms of unknown affinity, the remainder cover a broad taxonomic range of angiosperm trees and include members of several major clades: monocots (1 pollen type), fabids (7), malvids (4), asterids (5) and other core eudicots (1). Seven types each can be assigned to individual genera or infrafamilial clades. Since bees visit only flowers in the relative vicinity of their habitat, the recovered pollen provides a unique insight into the autochthonous palaeo-flora. The coexistence of taxa such as Decodon, Elaeocarpus, Mortoniodendron and other Tilioideae, Mastixoideae, Olax, Pouteria and Nyssa confirms current views that diverse, thermophilic forests thrived at the Messel and Eckfeld localities, probably under a warm subtropical, fully humid climate. Our study calls for increased attention to pollen found in situ on pollen-harvesting insects such as bees, which can provide new insights on insect-pollinated plants and complement even detailed palaeo-palynological knowledge obtained mostly from pollen of wind-pollinated plants in the dispersed pollen record of sediments. In the case of Elaeocarpus, Mortoniodendron, Olax and Pouteria the pollen collected by the middle Eocene bees represent the earliest unambiguous records of their respective genera.

Water lilies as emerging models for Darwin's abominable mystery

Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered 'an abominable mystery' by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin's 'abominable mystery'. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST.