Phylogenetic relationships in Asarum: Effect of data partitioning and a revised classification

A comparative analysis of plastome evolution in autotrophic Piperales

PREMISE

Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed.

METHODS

We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics.

RESULTS

We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region.

CONCLUSIONS

This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.

Total-evidence dating and morphological partitioning: a novel approach to understand the phylogeny and biogeography of augochlorine bees (Hymenoptera: Apoidea)

Augochlorini comprise 646 described bee species primarily distributed in the Neotropical region. According to molecular and morphological phylogenies, the tribe is monophyletic and subdivided into seven genus groups. Our main objective is to propose a revised phylogeny of Augochlorini based on a comprehensive data set including fossil species as terminals and new characters from the internal skeleton. We also aim to develop a total-evidence framework incorporating a morphological-partitioned homoplasy approach and molecular data and propose a detailed biogeographic and evolutionary scenario based on ancestor range estimation. Our results recovered Augochlorini and most genus groups as monophyletic, despite some uncertainties about monophyly of the Megalopta and Neocorynura groups. The position of the cleptoparasite Temonosoma is still uncertain. All analyses recovered Augochloropsis s.l. as related to the Megaloptidia group. Internal characters from the head, mesosoma and sting apparatus provided important synapomorphies for most internal nodes, genus groups and genera. Augochlorini diversification occurred in the uplands of the Neotropical region, especially the Brazilian Plateau. Multiple dispersals to Amazonia, Central America and North America with returns to the Atlantic endemism area were recovered in our analysis. Total evidence, including morphological partitioning, was shown to be a reliable approach for phylogenetic reconstruction.

Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses

The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.

The complete chloroplast genome of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. (Aristolochiaceae), a traditional Chinese medicine herb

The complete chloroplast genome of A. heterotropoides var. mandshuricum reported herein was a circular DNA molecule of 160,262 bp in length. The typical quadripartite structure of the genome consisted of a pair of inverted repeats (IRs) of 27,262 bp separated by a large single-copy (LSC) region of 88,927 bp and a small single-copy region (SSC) of 16,811 bp. The overall GC content of the genome is 38.45%, with 36.7%, 33.1%, and 43.0% in LSC, SSC, IR regions, respectively. The cp genome encoded 125 genes, including 83 protein-coding genes, 34 tRNA genes, and 8 rRNA genes. 138 SSRs were identified in the genome. Phylogenetic anlysis showed the position of A. heterotropoides var. mandshuricum is closely related to A. heterotropoides.

Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes

Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.

Seed dormancy and germination of Asarum sieboldii, a disjunct relict species in East Asia

Disjunct species in the same genus are a common feature of the flora in the temperate forests of East Asia and eastern North America. This study aimed to evaluate whether the kind of seed dormancy was maintained after species in the genus Asarum (Aristolochiaceae) were separated from their common ancestor. We classified the seed dormancy of Asarum sieboldii, an East Asian species, based on a phenology study and experiments in controlled temperature conditions, and then compared it to that of the previously studied A. canadense, an eastern North American species. The underdeveloped embryo of A. sieboldii grew and germinated (radicle emergence) in autumn but shoot emergence did not occur until the following spring. The seeds of A. sieboldii had deep simple epicotyl morphophysiological dormancy because the seeds with emerged radicle required a relatively long period of cold stratification to break epicotyl dormancy and produce a shoot. Although the seed of A. sieboldii had weaker radicle dormancy and stronger epicotyl dormancy compared to A. canadense, the kind of seed dormancy was the same for the two species. The trait of seed dormancy was inherited from a shared common ancestor and maintained in populations well after the two species (or their ancestors) separated. However, quantitative differences in temperature requirements for radicle and shoot emergence suggest the possibility of adaptation to the environment.

Radiation history of Asian Asarum (sect. Heterotropa, Aristolochiaceae) resolved using a phylogenomic approach based on double-digested RAD-seq data

BACKGROUND AND AIMS

The genus Asarum sect. Heterotropa (Aristolochiaceae) probably experienced rapid diversification into 62 species centred on the Japanese Archipelago and Taiwan, providing an ideal model for studying island adaptive radiation. However, resolving the phylogeny of this plant group using Sanger sequencing-based approaches has been challenging. To uncover the radiation history of Heterotropa, we employed a phylogenomic approach using double-digested RAD-seq (ddRAD-seq) to yield a sufficient number of phylogenetic signals and compared its utility with that of the Sanger sequencing-based approach.

METHODS

We first compared the performance of phylogenetic analysis based on the plastid matK and trnL-F regions and nuclear ribosomal internal transcribed spacer (nrITS), and phylogenomic analysis based on ddRAD-seq using a reduced set of the plant materials (83 plant accessions consisting of 50 species, one subspecies and six varieties). We also conducted more thorough phylogenomic analyses including the reconstruction of biogeographic history using comprehensive samples of 135 plant accessions consisting of 54 species, one subspecies, nine varieties of Heterotropa and six outgroup species.

KEY RESULTS

Phylogenomic analyses of Heterotropa based on ddRAD-seq were superior to Sanger sequencing-based approaches and resulted in a fully resolved phylogenetic tree with strong support for 72.0-84.8 % (depending on the tree reconstruction methods) of the branches. We clarified the history of Heterotropa radiation and found that A. forbesii, the only deciduous Heterotropa species native to mainland China, is sister to the evergreen species (core Heterotropa) mostly distributed across the Japanese Archipelago and Taiwan.

CONCLUSIONS

The core Heterotropa group was divided into nine subclades, each of which had a narrow geographic distribution. Moreover, most estimated dispersal events (22 out of 24) were between adjacent areas, indicating that the range expansion has been geographically restricted throughout the radiation history. The findings enhance our understanding of the remarkable diversification of plant lineages in the Japanese Archipelago and Taiwan.

Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum

PREMISE OF THE STUDY

As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes).

METHODS

Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum. Sequenced plastomes were compared in a phylogenetic context provided by maximum likelihood and parsimony inferences made using an additional 18 publicly available plastomes from early-diverging angiosperm lineages.

KEY RESULTS

In contrast to previously published magnoliid plastomes and the newly sequenced Saruma henryi plastome published here, Asarum plastomes have undergone extensive disruption and contain extremely lengthy AT-repeat regions. The entirety of the small single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii has been incorporated into the inverted repeat regions (IR), and the SSC of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an inversion of a large portion of the large single copy region (LSC) such that trnE-UUC is adjacent to the LSC-IR boundary.

CONCLUSIONS

Plastome divergence in Asarum appears to be consistent with trends seen in highly rearranged plastomes of the monocots and eudicots. We propose that plastome instability in Asarum is due to repetitive motifs that serve as recombinatory substrates and reduce genome stability.