Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era.

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae).

BACKGROUND: Crossostephium chinense is a traditional Chinese medicinal herb and it is often cultivated as an ornamental plant. Previous studies on this species mainly focused on its chemical composition and it was rarely represented in genetic studies, and thus genomic resources remain scarce. METHODS AND RESULTS: Both chloroplast and nuclear polymorphic microsatellites of C. chinense were screened from genome skimming data of two individuals. 64 and 63 cpSSR markers were identified from two chloroplast genomes of C. chinense. A total of 133 polymorphic nSSRs were developed. Ten nSSRs were randomly selected to test their transferability across 35 individuals from three populations of C. chinense, and 20 individuals each of Artemisia stolonifera and A. argyi. Cross-amplifications were successfully done for C. chinense and were partially amplified for both Artemisia species. The number of alleles varied from two to nine. The observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 0.286 and from 0.029 to 0.755, respectively. CONCLUSIONS: In this study, we developed polymorphic cpSSRs and nSSRs markers for C. chinense based on genome skimming sequencing. These genomic resources will be valuable for population genetics and conservation studies in C. chinense and Artemisia.

Salvia guidongensis sp. nov.: unraveling a critical evolutionary link in East Asian Salvia from Central China integrating morphology, phylogeny, and plastid genomics.

Introduction: Salvia L., representing the largest genus within the mint family, is noted for its global distribution of approximately 1000 species, with East Asia, and particularly China, recognized as a critical center of diversity for the genus. Methods: Our research was conducted through extensive fieldwork in Guidong County, Hunan Province, China, where we identified a previously undescribed species of Salvia. The identification process involved detailed morphological observations, phylogenetic analyses, and plastid genomics. Results: The newly discovered species, Salvia guidongensis, exhibits unique characteristics not commonly observed in the East Asian lineage of Salvia, including dual floral colors within natural populations-either pale purple or pale yellow. Morphologically, while it shares similarities with members of sect. Glutinaria, S. guidongensis is distinct in its floral morphology, stature, and specific foliar traits. Phylogenetic analysis places S. guidongensis in a unique clade within the East Asian lineage of Salvia, suggesting it may serve as an important evolutionary link. Additionally, we explored the plastome features of S. guidongensis, comparing them with those of closely related species. Discussion: The discovery of S. guidongensis not only entriches the taxonomic tapestry of Salvia but also provides critical insights into the biogeography and evolutionary pathways of the genus in East Asia. By integrating morphological and molecular data, we validate the novel status of S. guidongensis and highlight its significance in bridging taxonomic and evolutionary gaps within Sect. Glutinaria of Salvia.

Refining the phylogeny and taxonomy of the apple tribe Maleae (Rosaceae): insights from phylogenomic analyses of 563 plastomes and a taxonomic synopsis of Photinia and its allies in the Old World.

This study addresses the longstanding absence of a comprehensive phylogenetic backbone for the apple tribe Maleae, a deficiency attributed to limited taxon and marker sampling. We conducted an extensive taxon sampling, incorporating 563 plastomes from a diverse range of 370 species encompassing 26 presently recognized genera. Employing a range of phylogenetic inference methods, including RAxML and IQ-TREE2 for Maximum Likelihood (ML) analyses, we established a robust phylogenetic framework for the Maleae tribe. Our phylogenomic investigations provided compelling support for three major clades within Maleae. By integrating nuclear phylogenetic data with morphological and chromosomal evidence, we propose an updated infra-tribal taxonomic system, comprising subtribe Malinae Reveal, subtribe Lindleyinae Reveal, and subtribe Vauqueliniinae B.B.Liu (subtr. nov.). Plastid phylogenetic analysis also confirmed the monophyly of most genera, except for Amelanchier, Malus, Sorbus sensu lato, and Stranvaesia. In addition, we present a comprehensive taxonomic synopsis of Photinia and its morphological allies in the Old World, recognizing 27 species and ten varieties within Photinia, three species and two varieties within Stranvaesia, and two species and three varieties within Weniomeles. Furthermore, we also lectotypified 12 names and made two new combinations, Photiniamicrophylla (J.E.Vidal) B.B.Liu and Weniomelesatropurpurea (P.L.Chiu ex Z.H.Chen & X.F.Jin) B.B.Liu.

Malus includes Docynia (Maleae, Rosaceae): evidence from phylogenomics and morphology.

Docynia has been treated as a separate genus or merged into Cydonia or Docyniopsis. Our phylogenomic evidence from 797 single-copy nuclear genes and plastomes confirmed the sister relationship between Docynia and Docyniopsis. By integrating the phylogenomic and morphological evidence, we propose to accept a broad generic concept of Malus and merge Docynia into Malus. Three new combinations are also made here: Malusdelavayi (Franch.) B.B.Liu, M.indica (Wall.) B.B.Liu and M.longiunguis (Q.Luo & J.L.Liu) B.B.Liu.

Self-Distilled Supervised Contrastive Learning for diagnosis of breast cancers with histopathological images.

Convolutional neural networks (CNN) and its variants have been widely used for developing the histopathological image based computer-aided diagnosis (CAD). However, the annotated data are scarce in clinical practice, and limited training samples generally cannot well train the CNN model, resulting in degraded predictive performance. To this end, we propose a novel Self-Distilled Supervised Contrastive Learning (SDSCL) algorithm to improve the diagnostic performance of a CNN-based CAD for breast cancer. In particular, the original histopathological images are first decomposed into H and E stain views, which are served as the augmented sample pairs in the supervised contrastive learning (SCL). Due to the complementary characteristic of the two stain views, this data-driven SCL guide the CNN model to efficiently learn the discriminative features, alleviating the problem of small sample size. Furthermore, self-distillation is embedded into the SCL framework, in which the CNN model jointly distills itself and conducts SCL to further improve feature representation. The proposed SDSCL is evaluated on two public breast histopathological datasets, which outperforms all the compared algorithms. Its average classification accuracy, precision, recall, and F1 scores are 94.28%, 94.64%, 94.58%, 94.34%, respectively, on Bioimaging dataset, and 80.44%, 81.92%, 80.57%, 80.10% on Databiox dataset. The experimental results on two datasets indicate that SDSCL has the potential for the histopathological image based CAD.

Violashiweii, a new species of Viola (Violaceae) from karst forest in Guizhou, China.

Violashiweii Xiao C. Li & Z. W. Wang (Violaceae), a new species from Guizhou, China, is described, based on morphological and molecular evidence. The new species is morphologically most similar to V.kwangtungensis Melchior in its glabrous lateral petals and stoloniferous habit, but can be distinguished by its obtuse teeth along the leaf margin, its abaxially greyish-green leaf blade and its broader and entire sepals with a distinct basal appendage.

Begonia shenzhenensis, a new species of Begoniaceae from Guangdong, China.

Begonia shenzhenensis D.K.Tian & X.Yun Wang, sp. nov., a new species in Begonia sect. Platycentrum of Begoniaceae from Shenzhen of Guangdong province, China, is described and illustrated. Morphologically, it is primarily similar to B. coelocentroides in the same section but differs by its denser hairs on leaf, petiole, and pedicel, abtuse anther apex, hairy ovary, and narrower adaxial fruit wing. Based on only one small population found to date, its conservation status is assigned to Critical Endangered according to the IUCN Red List Categories and Criteria.

A new species (Begoniagiganticaulis) of Begoniaceae from southern Xizang (Tibet) of China.

Begoniagiganticaulis, a huge new species in Begoniasect.Platycentrum of Begoniaceae from southern Xizang (Tibet) of China, is described. Morphologically, it is mostly similar to B.longifolia and B.acetosella, but clearly differs from the former mainly by its dioecious and taller plants, sparse hairs on abaxial veins, longer inflorescence, unique shape of fruits, and differs from the latter mainly by its late and longer flowering time, 6-tepals of female flower and 3-loculed ovary. The phylogenetic analyses also support the separation of the new species from other taxa. Based on the current data, its conservation status is assigned to Endangered (B2a) according to the IUCN Red List Categories and Criteria.

The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway.

Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient, celastrol, is a friedelane-type pentacyclic triterpenoid with putative roles as an antitumor, immunosuppressive, and anti-obesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation using a hybrid sequencing strategy. The total genome size obtained is 340.12 Mb, with a contig N50 value of 3.09 Mb. We successfully anchored 91.02% of sequences into 23 pseudochromosomes using high-throughput chromosome conformation capture (Hi-C) technology. The super-scaffold N50 value was 13.03 Mb. We also annotated 31,593 structural genes, with a repeat percentage of 44.31%. These data demonstrate that T. wilfordii diverged from Malpighiales species approximately 102.4 million years ago. By integrating genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of two cytochrome P450 (CYP450) genes, TwCYP712K1 and TwCYP712K2, it is possible to investigate the second biosynthesis step of celastrol and demonstrate that this was derived from a common ancestor. These data provide insights and resources for further investigation of pathways related to celastrol, and valuable information to aid the conservation of resources, as well as understand the evolution of Celastrales.

Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae).

Relict species play an important role in understanding the biogeography of intercontinental disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on Pterocarya have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of Pterocarya using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of Pterocarya. Our results support the existence of two sections in Pterocarya, which is in accordance with morphological taxonomy. Section Platyptera comprises three species: P. rhoifolia, P. macroptera, and P. delavayi. Section Pterocarya also comprises three species: P. fraxinifolia, P. hupehensis, and P. stenoptera. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between P. hupehensis and P. stenoptera as well as between P. rhoifolia and P. macroptera/P. delavayi (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.