Phylogeny and Classification of Paris (Melanthiaceae) Inferred from DNA Sequence Data

• Background and Aims Paris (Melanthiaceae) is a temperate genus of about 24 perennial herbaceous species distributed from Europe to eastern Asia. The delimitation of the genus and its subdivisions are unresolved questions in the taxonomy of Paris. The objective of this study is to test the generic and infrageneric circumscription of Paris with DNA sequence data

Isolation and Characterization of Microsatellite Loci in Pistacia weinmannifolia (Anacardiaceae)

Fourteen polymorphic microsatellite loci were isolated from the genomic DNA of Pistacia weinmannifolia, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) method, and screened on 12 individuals from each of two wild populations. The 14 polymorphic loci had an average of 4.1 alleles per locus varying from 1 to 9. The observed (Ho) and expected (He) heterozygosities across the two populations ranged from 0.000 to 0.933 and from 0.000 to 0.906, respectively. Tests for departure from Hardy-Weinberg equilibrium (HWE) and genotypic linkage disequilibrium (LD) were conducted for each of the two populations separately. It was found that no locus significantly deviated from HWE proportions and no significant LD was detected between loci (p < 0.001). In the test of cross-species utility, we successfully amplified nine (64.2%) of 14 loci in P. chinensis and four (28.6%) in P. mexicana. The relatively high level of polymorphism for these markers will facilitate further studies of gene flow, population structure and evolutionary history of P. weinmannifolia and its congeners

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis

The Arcto-Tertiary relict genera, Camptotheca, Davidia, and Nyssa represent deep lineages in the asterid order Cornales. Recent phylogenetic studies suggested that these genera should be placed in a newly circumscribed family, Nyssaceae. However, because these analyses were based upon a few genes, it is prudent and necessary to examine further evidence before adopting this taxonomic treatment. In this study, we determined the complete chloroplast (cp) genomes of Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Their cp genomes ranged from 156,672 to 158,409 bp, which included 115 genes, and their genome features were highly similar to those of other species within the order Cornales. The phylogenetic relationships among the genera Camptotheca, Davidia, Nyssa, and 23 related taxa in the asterids were analyzed based on 73 protein-coding genes from the cp genomes. All of the previously recognized major clades (namely Cornales, Ericales, Campanulids, and Lamiids) in the asterids, as well as their relationships, were recovered with robust support. A clade including the genera Davidia, Nyssa, Camptotheca, and Diplopanax, was resolved as a well-supported monophyletic group, which was fully separated from the family Cornaceae by the family Hydrangeaceae. Our results provide novel evidence to support the acceptance of the family Nyssaceae outlined by the updated Angiosperm Phylogeny Group

Complete plastome of Toricellia tiliifolia (Toricelliaceae), a relict plant

In this study, we presented the first complete plastome of Toricellia tiliifolia, an Arcto-Tertiary relict endemic to eastern Asian, using Illumina pair-end sequencing data. The plastome was 158,627 bp in length and consisted of a pair of inverted repeats (IRs 26,174 bp), which were separated by a large single-copy region (LSC 87,847 bp) and a small single-copy region (SSC 18,432 bp). The plastome harbored 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenetic analysis indicated that T. tiliifolia was the earliest diverged clade within the order Apiales

Complete chloroplast genome of the economically important crop, Amorphophallus konjac (Araceae)

Konjac (Amorphophallus konjac K. Koch) is a perennial herb with high commercial and medicinal values. To better understand its genetic and genomic profiles, we sequenced and assembled the completed chloroplast genome of A. konjac. The complete chloroplast genome is 155,277 bp in length, consisting of the large (LSC, 85,412 bp) and the small single-copy region (SSC, 19,449 bp), which were separated by a pair of inverted repeat regions (IRs, 25,208 bp). It possesses 113 unique genes (80protein-coding genes, 29 tRNAs and 4rRNAs). Phylogenetic analysis suggests that A. konjac is closely related to Colocasia esculenta and Pinellia ternata

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)

Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species. Keywords: Araliaceae, Plastome, Comparative genomics, Panax stipuleanatus, Phylogenomic

Characterization of the whole plastome of Dipentodon Sinicus (Dipentodontaceae)

In this study, we sequenced and assembled the whole plastome of Dipentodon sinicus. The plastome was 158,020 bp in length and consisted of a pair of inverted repeat regions (IRs, 26,551 bp), a large single-copy region (LSC, 86,624 bp) and a small single-copy region (SSC, 18,294 bp). It encoded 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). Phylogenetic analysis showed that Dipentodon sinicus was sister to Tapiscia sinensis

Phylogeny and Classification of Paris (Melanthiaceae) Inferred from DNA Sequence Data

• Background and Aims Paris (Melanthiaceae) is a temperate genus of about 24 perennial herbaceous species distributed from Europe to eastern Asia. The delimitation of the genus and its subdivisions are unresolved questions in the taxonomy of Paris. The objective of this study is to test the generic and infrageneric circumscription of Paris with DNA sequence data. • Methods Phylogenetic analysis of 21 species of Paris based on nuclear ITS and plastid psbA-trnH and trnL-trnF DNA sequence data, alone and in combination, was employed to assess previous classifications. • Key Results Paris is monophyletic in all analyses. Neither of the two traditionally recognized subgenera (Paris and Daiswa) are monophyletic. Sections Axiparis, Kinugasa, Paris and Thibeticae are monophyletic in only some of the analyses. Species of sections Dunnianae, Fargesianae and Marmoratae are consistently intercalated among species of section Euthyra in all analyses. Strong discordance between nuclear and plastid lineages is detected. • Conclusions The data support the classification of Paris as a single genus rather than as three genera (Daiswa, Kinugasa and Paris sensu stricto). They provide justification for the transfer of section Axiparis from subgenus Paris to subgenus Daiswa and for the combination of sections Dunnianae, Fargesianae and Marmoratae into section Euthyra. The nuclear-plastid discordance is interpreted as the result of interspecific hybridization among sympatric species

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Saxifragales

Abstract Background The “woody clade” in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence. Results Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. Conclusions Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships

Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere