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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. [ABSTRACT FROM AUTHOR]

Multichromosomal mitochondrial genome (mitogenome) structures have repeatedly evolved in many lineages of angiosperms. However, the underlying mechanism remains unclear. The mitogenomes of three genera of Balanophoraceae, namely Lophophytum , Ombrophytum , and Rhopalocnemis , have already been sequenced and assembled, all showing a highly multichromosomal structure, albeit with different genome and chromosome sizes. It is expected that characterization of additional lineages of this family may expand the knowledge of mitogenome diversity and provide insights into the evolution of the plant mitogenome structure and size. Here, we assembled and characterized the mitogenome of Thonningia sanguinea , which, together with Balanophora , forms a clade sister to the clade comprising Lophophytum , Ombrophytum , and Rhopalocnemis. The mitogenome of T. sanguinea possesses a multichromosomal structure of 18 circular chromosomes of 8.7–19.2 kb, with a total size of 246,247 bp. There are very limited shared regions and poor chromosomal correspondence between T. sanguinea and other Balanophoraceae species, suggesting frequent rearrangements and rapid sequence turnover. Numerous medium- and small-sized repeats were identified in the T. sanguinea mitogenome; however, no repeat-mediated recombination was detected, which was verified by Illumina reads mapping and PCR experiments. Intraspecific mitogenome variations in T. sanguinea are mostly insertions and deletions, some of which can lead to degradation of perfect repeats in one or two accessions. Based on the mitogenome features of T. sanguinea , we propose a mechanism to explain the evolution of a multichromosomal mitogenome from a master circle, which involves mutation in organellar DNA replication, recombination and repair genes, decrease of recombination, and repeat degradation. [ABSTRACT FROM AUTHOR]

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial--interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages. [ABSTRACT FROM AUTHOR]

Piperales is among the largest and most diverse angiosperm orders (>4000 species), occurring broadly in tropical and temperate habitats. Twenty-four of the species from 12 genera, representing all lineages of Piperales, except the holoparasitic Hydnoraceae, display a mixture of leaf calcium oxalate crystal types found in previous studies of the two genera of Piperaceae subfamily Piperoideae (Peperomia Ruiz & Pav. and Piper L.). Crystal macropatterns, a result of varying leaf anatomies and diverse habitats, are investigated in a comparative way by using clearings and recent molecular phylogenetic hypotheses to trace crystal types and macropattern evolution. Ancestral character reconstruction reveals that the most recent common ancestor of Piperales had either crystal sand or druses or both and that prisms, raphides, and styloids are derived from the ancestral crystal type(s). These results are also recovered for both the ancestors of the perianth-less and the perianth-bearing Piperales. Raphides or druses are found in the two other subfamilies of Piperaceae (Verhuellioideae and Zippelioideae). Asaraceae and Lactoridaceae display crystal sand, whereas Aristolochia L. (Aristolochiaceae) species display mainly druses. Our crystal investigation, combined with ancestral character reconstruction, suggests that styloids, raphides, and prisms are derived within Piperales from crystal sand or druses. Key words: calcium oxalate, crystals, leaf, macropatterns, Piperales lineages. Les piperales (Piperales) constituent un des ordres d'angiospermes le plus grand et le plus diversifie (>4000 especes), trouvees largement dans des habitats tropicaux et temperes. Vingt-quatre des especes provenant de 12 genres, qui representent tous les lignages des Piperales, hormis les Hydnoraceae holoparasites, presentent un melange de types de cristaux foliaires d'oxalate de calcium selon des etudes precedentes realisees sur deux genres des Piperales sous-famille Piperoideae (Peperomia Ruiz & Pav. et Piper L.). Les macro-patrons des cristaux, qui resultent des variations anatomiques des feuilles et des differents habitats, sont examines de maniere comparative par clearing et selon des hypotheses phylogenetiques recentes, afin de suivre les types de cristaux et l'evolution des macro-patrons. La reconstruction des caracteres ancestraux revele que l'ancetre commun le plus recent des Piperales possedait soit du sable cristallin ou des druses ou les deux, et que les prismes, les raphides et les styloides sont derives du ou des types de cristaux ancestraux. Ces resultats sont aussi trouves a partir des deux ancetres des Piperales avec ou sans perianthe. Les raphides ou les druses sont trouves chez les deux autres sous-familles de Piperaceae (Verhuellioideae et Zippelioideae). Les Asaraceae et les Lactoridaceae comportent du sable cristallin, alors qu'Aristolochia L. (Aristolochiaceae) comporte principalement des druses. Les observations des cristaux realisees par les auteurs, combinees a la reconstruction du caractere ancestral, suggerent que les styloides, les raphides et les prismes sont derives du sable cristallin ou des druses chez les Piperales. [Traduit par la Redaction] Mots-cles : oxalate de calcium, cristaux, feuilles, macro-patrons, lignages de Piperales., Introduction Calcium oxalate crystals occur in green algae (Pueschel 2001; Leliaert and Coppejans 2004; Pueschel and West 2007), fungi (Arnott 1995), ferns (Poirault 1893; H.T. Horner, unpublished data), gymnosperms (Fink [...]

Background: Balanophoraceae plastomes are known for their highly condensed and re-arranged nature alongside the most extreme nucleotide compositional bias known to date, culminating in two independent reconfigurations of their genetic code. Currently, a large portion of the Balanophoraceae diversity remains unexplored, hindering, among others, evolutionary pattern recognition. Here, we explored newly sequenced plastomes of Sarcophyte sanguinea and Thonningia sanguinea. The reconstructed plastomes were analyzed using various methods of comparative genomics based on a representative taxon sampling. Results: Sarcophyte, recovered sister to the other sampled Balanophoraceae s. str., has plastomes up to 50% larger than those currently published. Its gene set contains five genes lost in any other species, including matK. Five cis-spliced introns are maintained. In contrast, the Thonningia plastome is similarly reduced to published Balanophoraceae and retains only a single cis-spliced intron. Its protein-coding genes show a more biased codon usage compared to Sarcophyte, with an accumulation of in-frame TAG stop codons. Structural plastome comparison revealed multiple, previously unknown, structural rearrangements within Balanophoraceae. Conclusions: For the "minimal plastomes" of Thonningia, we propose a genetic code change identical to sister genus Balanophora. Sarcophyte however differs drastically from our current understanding on Balanophoraceae plastomes. With a less-extreme nucleotide composition, there is no evidence for an altered genetic code. Using comparative genomics, we identified a hotspot for plastome reconfiguration in Balanophoraceae. Based on previously published and newly identified structural reconfigurations, we propose an updated model of evolutionary plastome trajectories for Balanophoraceae, illustrating a much greater plastome diversity than previously known. [ABSTRACT FROM AUTHOR]

The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea , Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus , a member of the perianth-less Piperales. The average number of short repeats (50–99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis - to trans -splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox 1 and atp 8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general. [ABSTRACT FROM AUTHOR]