The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent "series". Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (1) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (2) among all 42 sections and five "series", 25 sections and one "series" are resolved as monophyletic in both data sets; (3) the common ancestor of Corydalis was likely a perennial plant with a taproot, yellow flowers with short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (4) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncover previously unrecognized relationships, and greatly improve our understanding of the evolution of the genus. This article is protected by copyright. All rights reserved.

An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence.

ABSTRACT Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum , and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention. 

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution.

Abstract In the Flora of China account of Saxifraga mengtzeana Engl. & Irmsch., eight synonyms were attributed to it and one variant, recognized as Saxifraga epiphylla Gornall & Ohba, was split from it. This study reevaluates the taxonomic status of some of the synonyms and of the segregated species in light of new evidence presented here. Morphological and molecular evidence demonstrate that collections from northwestern Yunnan and Sichuan are genetically differentiated from those in southeastern Yunnan and neighboring Guangxi. Observations in the field and in cultivation show that the peltate petiole attachment diagnostic of S. mengtzeana var. peltifolia Engl. & Irmsch. is developmentally labile. Similar observations combined with molecular data show that viviparous phenotypes, formerly treated as S. epiphylla, although largely under genetic control, occur sporadically throughout the ranges of both northern and southern taxa. Collections from northwestern Yunnan and Sichuan are best recognized as Saxifraga geifolia Balf.f., whereas those from southeastern Yunnan and neighboring Guangxi are S. mengtzeana. Peltate‐leaved variants of the latter are given no status and are relegated to complete synonymy. Viviparous phenotypes of S. mengtzeana and S. geifolia are recognized at the rank of forma.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ece3.9886

A re‐examination of the circumscription of Saxifraga mengtzeana (Saxifragaceae)

Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.

RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic.

﻿Abstract A new species Sinosenecioyangii D.G. Zhang & Q. Zhou (Asteraceae, Senecioneae) from Guizhou Province, China, is described and illustrated based on its morphological characteristics and molecular evidence. It closely resembles S.confervifer and S.guangxiensis, the former in the scapigerous habit and smooth and glabrous achene surface, the latter in the calyculate involucre and purple abaxial leaf surface, and both in the shape and indumentum of leaf lamina, but differs markedly from the latter two in having fewer capitula and epappose achenes. Phylogenetic analysis based on nrITS and ndhC-trnV sequences shows that this new species belongs to the S.latouchei clade and is sister to S.guangxiensis with moderate support.

https://phytokeys.pensoft.net/article/89480/download/pdf/

﻿Sinosenecioyangii (Asteraceae), a new species from Guizhou, China

Climatic niche divergence and long-distance dispersal contributed to the pantropical intercontinental disjunctions of a liana lineage (Uncaria, Rubiaceae)

Saxifraga cataphracta, a new species of Saxifragaceae from Southwest China, is described and illustrated. Morphological and molecular evidence (matK, psbA-trnH, psaJ-rpl33) indicate that S. cataphracta belongs in S. sect. Irregulares, and is closely related to S. geifolia and S. mengtzeana. The new species can be diagnosed by its leaf blade abaxially with white or virescent interveinal streaks, involucre and bracts conspicuous, and capsule beaks winged when mature. 

Saxifraga cataphracta (Saxifragaceae), a new species from Southwest China

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An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence.

A re‐examination of the circumscription of Saxifraga mengtzeana (Saxifragaceae)

Sinosenecioyangii (Asteraceae), a new species from Guizhou, China

Climatic niche divergence and long-distance dispersal contributed to the pantropical intercontinental disjunctions of a liana lineage (Uncaria, Rubiaceae)

Saxifraga cataphracta (Saxifragaceae), a new species from Southwest China

Jun-Tong Chen

Author Tools

Chat about Author

Papers

An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence.

A re‐examination of the circumscription of Saxifraga mengtzeana (Saxifragaceae)

﻿Sinosenecioyangii (Asteraceae), a new species from Guizhou, China

Climatic niche divergence and long-distance dispersal contributed to the pantropical intercontinental disjunctions of a liana lineage (Uncaria, Rubiaceae)

Saxifraga cataphracta (Saxifragaceae), a new species from Southwest China

Sinosenecioyangii (Asteraceae), a new species from Guizhou, China