Systematics Research Articles

MOF-mediated acetylation of CDK9 promotes global transcription by modulating P-TEFb complex formation.

Cyclin-dependent kinase 9 (CDK9), a catalytic subunit of the positive transcription elongation factor b (P-TEFb) complex, is a global transcriptional elongation factor associated with cell proliferation. CDK9 activity is regulated by certain histone acetyltransferases, such as p300, GCN5 and P/CAF. However, the impact of males absent on the first (MOF) (also known as KAT8 or MYST1) on CDK9 activity has not been reported. Therefore, the present study aimed to elucidate the regulatory role of MOF on CDK9. We present evidence from systematic biochemical assays and molecular biology approaches arguing that MOF interacts with and acetylates CDK9 at the lysine 35 (i.e. K35) site, and that this acetyl-group can be removed by histone deacetylase HDAC1. Notably, MOF-mediated acetylation of CDK9 at K35 promotes the formation of the P-TEFb complex through stabilizing CDK9 protein and enhancing its association with cyclin T1, which further increases RNA polymerase II serine 2 residues levels and global transcription. Our study reveals for the first time that MOF promotes global transcription by acetylating CDK9, providing a new strategy for exploring the comprehensive mechanism of the MOF-CDK9 axis in cellular processes.

Development of a green Komagataella phaffii cell factory for sustainable production of plant-derived sesquiterpene (–)-α-bisabolol

(–)-α-Bisabolol is a plant-derived sesquiterpene derived from Eremanthus erythropappus, which can be used as a raw material in cosmetics and has anti-inflammatory function. In this study, we designed six mutation sites of the (–)-α-bisabolol synthase BOS using the plmDCA algorithm. Among these, the F324Y mutation demonstrated exceptional performance, increasing the product yield by 73 %. We constructed a de novo (–)-α-bisabolol biosynthesis pathways through systematic synthetic biology strategies, including the enzyme design of BOS, selection of different linkers in fusion expression, and optimization of the mevalonate pathway, weakening the branching metabolic flow and multi-copy strategies, the yield of (–)-α-bisabolol was significantly increased, which was nearly 35-fold higher than that of the original strain (2.03 mg/L). The engineered strain was capable of producing 69.7 mg/L in shake flasks. To the best of our knowledge, this is the first report on the biosynthesis of (–)-α-bisabolol in Komagataella phaffii, implying this is a robust cell factory for sustainable production of other terpenoids.

The Democratization of Systematic Biology

The Democratization of Systematic Biology

Inferring Taxonomic Affinities and Genetic Distances Using Morphological Features Extracted from Specimen Images: a Case Study with a Bivalve dataset.

Reconstructing the tree of life and understanding the relationships of taxa are core questions in evolutionary and systematic biology. The main advances in this field in the last decades were derived from molecular phylogenetics; however, for most species, molecular data are not available. Here, we explore the applicability of two deep learning methods - supervised classification approaches and unsupervised similarity learning - to infer organism relationships from specimen images. As a basis, we assembled an image dataset covering 4144 bivalve species belonging to 74 families across all orders and subclasses of the extant Bivalvia, with molecular phylogenetic data being available for all families and a complete taxonomic hierarchy for all species. The suitability of this dataset for deep learning experiments was evidenced by an ablation study resulting in almost 80% accuracy for identifications on the species level. Three sets of experiments were performed using our dataset. First, we included taxonomic hierarchy and genetic distances in a supervised learning approach to obtain predictions on several taxonomic levels simultaneously. Here, we stimulated the model to consider features shared between closely related taxa to be more critical for their classification than features shared with distantly related taxa, imprinting phylogenetic and taxonomic affinities into the architecture and training procedure. Second, we used transfer learning and similarity learning approaches for zero-shot experiments to identify the higher-level taxonomic affinities of test species that the models had not been trained on. The models assigned the unknown species to their respective genera with approximately 48% and 67% accuracy. Lastly, we used unsupervised similarity learning to infer the relatedness of the images without prior knowledge of their taxonomic or phylogenetic affinities. The results clearly showed similarities between visual appearance and genetic relationships at the higher taxonomic levels. The correlation was 0.6 for the most species-rich subclass (Imparidentia), ranging from 0.5 to 0.7 for the orders with the most images. Overall, the correlation between visual similarity and genetic distances at the family level was 0.78. However, fine-grained reconstructions based on these observed correlations, such as sister-taxa relationships, require further work. Overall, our results broaden the applicability of automated taxon identification systems and provide a new avenue for estimating phylogenetic relationships from specimen images.

Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.

Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

Abstract IA022: Mechanisms of splicing dysregulation and dependency in cancer

Abstract Dysregulated RNA splicing is a hallmark feature of cancer. Much like mutational signatures in tumors, RNA mis-splicing patterns are widely heterogeneous and segregate tumors into clades, suggesting there are distinct mechanisms underlying these splicing aberrations. However, the mechanisms driving such distinct RNA splicing dysregulation remain largely unknown. Herein, we discovered that copy-number variation of essential splicing factors is a pervasive cause of splicing dysregulation, and in some tumor contexts, confers deep dependencies on RNA-binding proteins (RBPs) that converge on these mechanisms. Using a systematic chemical biology approach, we delineate how splicing RBPs participate in distinct types of RNA quality control in cells, and when disrupted, produce surprisingly unique patterns of RNA mis-splicing. These RBP-specific mis-splicing patters are common in distinct cancer types. Notably, unbiased genome-wide analysis revealed that RBP-specific mis-splicing patterns found in tumors were significantly associated with copy number loss of a network of functionally linked splicing factors. These splicing factors often reside on tumor suppressor loci that are frequently deleted in breast and other cancers, suggesting that copy number loss of essential splicing RBPs is a collateral event with selected loss of tumor suppressors. Importantly, RBP-specific mis-splicing signatures also segregate tumor models that are dependent on the concordant RBP, suggesting that these tumors evolve defects in RBP function that predispose them to further perturbation. Together, our work suggests that deletions of tumor suppressor loci may drive collateral dysregulation of RNA splicing through partial loss of splicing RBPs and provokes the hypothesis that these mis-splicing signatures may predict actionable dependencies in the cancers that harbor them. Citation Format: Kristen Karlin. Mechanisms of splicing dysregulation and dependency in cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA022.

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus.

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.

Comprehensive multi-omics analysis and experimental verification reveal PFDN5 is a novel prognostic and therapeutic biomarker for gastric cancer

Prefoldin Subunit 5 (PFDN5) plays a critical role as a member of the prefoldins (PFDNs) in maintaining a finely tuned equilibrium between protein production and degradation. However, there has been no comprehensive analysis specifically focused on PFDN5 thus far. Here, a comprehensive multi-omics (transcriptomics, genomics, and proteomics) analysis, systematic molecular biology experiments (in vitro and in vivo), transcriptome sequencing and PCR Array were performed for identifying the value of PFDN5 in pan-cancer, especially in Gastric Cancer (GC). We found PFDN5 had the potential to serve as a prognostic and therapeutic biomarker in GC. And PFDN5 could promote the proliferation of GC cells, primarily by affecting the cell cycle, cell death and immune process etc. These findings provide novel insights into the molecular mechanisms and precise treatments of in GC.

Mechanistic causes of sign epistasis and its applications.

Mapping genetic variations to phenotypic variations poses a significant challenge, as mutations often combine unexpectedly, diverging from assumed additive effects even in the same environment. These interactions are known as epistasis or genetic interactions. Sign epistasis, as a specific type of epistasis, involves a complete reversal of mutation effects within altered genetic backgrounds, presenting a substantial hurdle to phenotype prediction. Despite its importance, there is a limited systematic overview of the mechanistic causes of sign epistasis. This review explores the mechanistic causes, highlighting its occurrence in signalling cascades, peaked fitness landscapes, and physical interactions. Moving beyond theoretical discussions, we delve into the practical applications of sign epistasis in agriculture, evolution, and antibiotic resistance. In conclusion, this review aims to enhance the comprehension of sign epistasis and molecular dynamics, anticipating future endeavours in systematic biology engineering that leverage the knowledge of sign epistasis.

Simultaneous dual-region two-photon imaging of biological dynamics spanning over 9 mm in vivo

Biodynamical processes, especially in system biology, that occur far apart in space may be highly correlated. To study such biodynamics, simultaneous imaging over a large span at high spatio-temporal resolutions is highly desired. For example, large-scale recording of neural network activities over various brain regions is indispensable in neuroscience. However, limited by the field-of-view (FoV) of conventional microscopes, simultaneous recording of laterally distant regions at high spatio-temporal resolutions is highly challenging. Here, we propose to extend the distance of simultaneous recording regions with a custom micro-mirror unit, taking advantage of the long working distance of the objective and spatio-temporal multiplexing. We demonstrate simultaneous dual-region two-photon imaging, spanning as large as 9 mm, which is 4 times larger than the nominal FoV of the objective. We verify the system performance in in vivo imaging of neural activities and vascular dilations, simultaneously, at two regions in mouse brains as well as in spinal cords, respectively. The adoption of our proposed scheme will promote the study of systematic biology, such as system neuroscience and system immunology.

Olfactory receptors in Bactrocera species for sustainable fruit fly management: A review and future perspectives

AbstractMolecular studies on odorant receptors (ORs), odorant‐binding proteins (OBPs) and the functioning of the receptor and pheromone signal transduction in fruit fly Bactrocera species have expanded exponentially during the past few decades. OBPs contribute to the sensing of the olfactory system (OS) via the transduction of odorants through the sensillum lymph. However, ORs, a family of G‐protein‐coupled receptors in Bactrocera and various other species, exhibit heightened responsiveness to multiple chemical odours such as hormones, sensory stimuli and neurotransmitters. The apparent mechanism involves a combinatorial code encompassing both peripheral and antennal lobe processing, facilitating the reception of sexual pheromones and environmental cues. The OS is specifically designed to recognize and process information from volatile chemical signals, and these chemical signals play an important function in various flies. Insects rely on these chemicals to navigate and comprehend their surroundings. A mature insect OS is composed of two pairs of sensillae‐covered palps, antennae and two primary pairs of olfactory appendages on the anterior head. It has been shown that chemosensory gene families contribute in odour perception. These include various neuroreceptor families, such as OBPs, chemosensory proteins and sensory neuron membrane proteins. Additionally, there are three divergent chemoreceptors, namely ORs, ionotropic receptors and gustatory receptors. Methods based on systematic biology, molecular biology and bioinformatics tools have rapidly emerged to investigate the insect communication systems and provide new insights for the management of many agricultural pest. Several aromatic compounds, including semiochemicals and pheromones, have been employed to defend crops and animals from destructive fruit flies and other invasive and frugivorous species. To promote the expansion of the cropping system, the utilization of phytochemical lures can be convenient for sustainable agriculture production and enhance food security. Hence, this review examined the state of the art in chemical communication of insects with a focus on fruit fly pest species to identify OS and their semiochemical receptors, protein receptors and chemosensory receptors (CSRs), as well as their practical applications for biological control and integrated pest management are highlighted.

First genome size assessment and fluorochrome chromosome banding in Argania spinosa (L.) Skeels (Sapotaceae)

ABSTRACT Argania is a monotypic genus belonging to the family Sapotaceae and comprising the only species Argania spinosa. This taxon, endemic to southern Morocco (northern Africa), is important in arid lands. It has a high pastoral value, numerous traditional uses, and it is an important industrial crop for food and cosmetics. A few chromosome counts are available for the species but to date, there is no information on its genome size. Apart from being a parameter useful in many aspects of plant systematic and evolutionary biology, knowing the nuclear DNA amount is a pre-requisite to any genome-sequencing program. In this paper, we present for the first time data on the nuclear DNA content in Argania spinosa, from two populations, and we confirm its chromosome number. Genome size was estimated as 2C = 1.48 pg (1C = 723.72 Mbp) in both studied accessions, revealing a small genome. The chromosome count (2n = 20) revealed that the species has the lowest basic chromosome number (x = 10) in the Sapotaceae, and suggests a descending dysploidy process in the family. The first morphological characterisation of Argania spinosa’s karyotype is presented here. In addition, fluorochrome banding, performed with chromomycin A3 and DAPI, showed the absence of AT-rich regions and the presence of GC-rich regions located in three chromosome pairs, bringing the first molecular cytogenetic data in the genus.

Hub Gene Mining and Co-Expression Network Construction of Low-Temperature Response in Maize of Seedling by WGCNA.

Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of maize response to low-temperature stress at the seedling stage, B144 (cold stress tolerant) and Q319 (cold stress sensitive) provided by the Maize Research Institute of Heilongjiang Academy of Agricultural Sciences were used as experimental materials, and both inbred lines were treated with 5 °C for 0 h, 12 h, and 24 h, with the untreated material as a control. Eighteen leaf samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, co-expression networks of weighted genes associated with low-temperature-tolerance traits were constructed by WGCNA. Twelve gene modules significantly related to low-temperature tolerance at the seedling stage were obtained, and a number of hub genes involved in low-temperature stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of low-temperature tolerance in maize at the seedling stage.

AIRFLOW ANALYSIS OF HUMAN RESPIRATORY SYSTEM AT DIFFERENT PHYSIOLOGICAL CONDITIONS

In this paper, an attempt has been made to analyze the effect of different physiological conditions i.e., rest, moderate and extremely active on the branch Reynolds number, pressure drop, lost work, alveolar partial O2 pressure, airway resistance and surface tension. From the analysis, it has been observed that local Reynolds number and tracheal pressure drop along with the generations of branch. The alveolar O2 pressure and surface tension decrease with the increased activity level. Work lost due to different major and minor losses in the respiratory tract increases with the increase in activity level. A similar trend was also found for the airway resistance i.e., increases with the increase in activity level. A new parameter, Breathing Work Number (BWN) in respiratory mechanics is introduced. BWN is the ratio of the work of breathing to the sum of work of breathing and work loss, which might find a significant application to denote the respiratory health. From the analysis, it is found that BWN decreases with the increase in activity level.

Variation in North American bumble bee nest success and colony sizes under captive rearing conditions.

Of the 265 known bumble bee (Bombus) species, knowledge of colony lifecycle is derived from relatively few species. As interest in Bombus commercialization and conservation grows, it is becoming increasingly important to understand colony growth dynamics across a variety of species since variation exists in nest success, colony growth, and reproductive output. In this study, we reported successful nest initiation and establishment rates of colonies and generated a timeline of colony development for 15 western North American Bombus species, which were captively reared from wild-caught gynes from 2009 to 2019. Additionally, we assessed variation in colony size among 5 western North American Bombus species from 2015 to 2018. Nest initiation and establishment rates varied greatly among species, ranging from 5-76.1% and 0-54.6%, respectively. Bombus griseocollis had the highest rates of nest success across the 11-yr period, followed by B. occidentalis, B. vosnesenskii, and B. huntii. Furthermore, days to nest initiation and days to nest establishment varied among species, ranging from 8.4 to 27.7 days and 32.7 to 47 days. Colony size also differed significantly among species with B. huntii and B. vosnesenskii producing more worker/drone cells than B. griseocollis, B. occidentalis, and B. vancouverensis. Additionally, gyne production differed significantly among species with B. huntii colonies producing more gynes than B. vosnesenskii. Results from this study increase knowledge of systematic nesting biology for numerous western North American Bombus species under captive rearing conditions, which can further improve rearing techniques available to conservationists and researchers.

Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.

In silico identification of potential miRNAs -mRNA inflammatory networks implicated in the pathogenesis of COVID-19

COVID-19 has been found to affect the expression profile of several mRNAs and miRNAs, leading to dysregulation of a number of signaling pathways, particularly those related to inflammatory responses. In the current study, a systematic biology procedure was used for the analysis of high-throughput expression data from blood specimens of COVID-19 and healthy individuals. Differentially expressed miRNAs in blood specimens of COVID-19 vs. healthy specimens were then identified to construct and analyze miRNA–mRNA networks and predict key miRNAs and genes in inflammatory pathways. Our results showed that 171 miRNAs were expressed as outliers in box plot and located in the critical areas according to our statistical analysis. Among them, 8 miRNAs, namely miR-1275, miR-4429, miR-4489, miR-6721-5p, miR-5010-5p, miR-7110-5p, miR-6804-5p and miR-6881–3p were found to affect expression of key genes in NF-KB, JAK/STAT and MAPK signaling pathways implicated in COVID-19 pathogenesis. In addition, our results predicted that 25 genes involved in above-mentioned inflammatory pathways were targeted not only by these 8 miRNAs but also by other obtained miRNAs (163 miRNAs). The results of the current in silico study represent candidate targets for further studies in COVID-19.

FREQUENCY OF METABOLIC SYNDROME IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS PRESENTING AT A PUBLIC SECTOR TERTIARY CARE HOSPITAL OF LAHORE: A CROSS- SECTIONAL STUDY

Background and Objective: Metabolic syndrome is characterized by central obesity, deranged lipid profile, high blood pressure and abnormally high levels of blood sugar. It is an independent risk factor for cardiovascular disease. Systemic Lupus Erythematosus (SLE) is an autoimmune disease that can affect joints, skin, brain, lungs, kidneys, and blood vessels. The extent to which metabolic syndrome is frequent in our population is less known. The objective of this study was to assess the frequency of metabolic syndrome amongst SLE patients. Methods: This cross-sectional study was undertaken in a public sector tertiary care hospital of Lahore from February 2021 through August 2021, including 110 confirmed SLE cases. After institutional approval and taking an informed consent, blood pressure, fasting and random blood sugar levels and fasting lipid profile were measured. Central obesity was assessed using waist circumference. Data were transferred to SPSS 21 for descriptive and inferential analyses. Frequencies were determined using numbers and percentages. Results: Of 110 SLE patients, 14 (12.3%) were males and 96 (87.7%) were females. Mean age of SLE patients was 42.9± 9.9 years. Mean BMI was 28.7±4.7 kg/m2. The frequency of metabolic syndrome in studied SLE patients was 37/110 (33.6%). Conclusion: Systemic lupus erythematosus patients had abnormally high serum triglyceride and cholesterol levels, diabetes mellitus, central obesity, high levels of fasting plasma glucose and hypertension. Therefore, one-third of SLE patients may have metabolic syndrome in our population.

Sporogenesis, gametophyte development and embryogenesis in Glehnia littoralis

BackgroundGlehnia littoralis is an economic herb with both medicinal and edible uses. It also has important ecological value and special phylogenetic status as it is a monotypic genus species distributing around beach. Little information on its reproductive biology has been reported so far, which has hindered conservation and application of this species. In this study, we observed morphological changes from buds emergence to seeds formation and internal changes during sporogenesis, gametophyte development and embryo and endosperm development of G. littoralis using paraffin-embedded-sectioning and stereo microscope.ResultsThe results showed that the stages of internal development events of G. littoralis corresponded to obvious external morphological changes, most of developmental features were consistent with other Apiaceae species. The development of male and female gametophytes was not synchronized in the same flower, however, exhibited temporal overlap. From mid-late April to mid-May, the anther primordial and ovule primordial developed into the trinucleate pollen grain and eight-nuclear embryo sac, respectively. From late-May to mid-July, the zygote developed into mature embryo. In addition, some defects in gynoecium or ovule development and abnormal embryo and endosperm development were found. We induced that the possible causes of abortion in G. littoralis were as follows: nutrient limitation, poor pollination and fertilization, and bad weather.ConclusionsThis study revealed the whole process and morphological characteristics of the development of reproductive organ in G. littoralis, which not only provided important data for the study of systematic and conservation biology, but also provided a theoretical basis for cross breeding.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data.

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s. l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene while dispersal into South America likely occurred during the Neogene. Diversification within the Northern Hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following the PhyloCode. Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names. This article is protected by copyright. All rights reserved.