Phenotype Research Articles

Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype.

It is well-known that the use of vocabulary in phenotype treatments is often inconsistent. An earlier survey of biologists who create or use phenotypic characters revealed that this lack of standardization leads to ambiguities, frustrating both the consumers and producers of phenotypic data. Such ambiguities are challenging for biologists, and more so for Artificial Intelligence, to resolve. That survey also indicated a strong interest in a new authoring workflow supported by ontologies to ensure published phenotype data are FAIR (Findable, Accessible, Interoperable, and Reusable) and suitable for large-scale computational analyses. In this article, we introduce a prototype software system designed for authors to produce computational phenotype data. This platform includes a web-based, ontology-enhanced editor for taxonomic characters (Character Recorder), an Ontology Backend holding standardized vocabulary (the Cared Ontology), and a mobile application for resolving ontological conflicts (Conflict Resolver). We present two formal user evaluations of Character Recorder, the main interface authors would interact with to produce FAIR data. The evaluations were conducted with undergraduate biology students and Carex experts. We evaluated Character Recorder against Microsoft Excel on their effectiveness, efficiency, and the cognitive demands of the users in producing computable taxon-by-character matrices. The evaluations showed that Character Recorder is quickly learnable for both student and professional participants, with its cognitive demand comparable to Excel's. Participants agreed that the quality of the data Character Recorder yielded was superior. Students praised Character Recorder's educational value, while Carex experts were keen to recommend it and help evolve it from a prototype into a comprehensive tool. Feature improvements recommended by expert participants have been implemented after the evaluation.

Correlation and Path Coefficient Studies of Yield and Its Contributing Traits in Groundnut (Arachis hypogea L.)

Groundnut is currently a major industrial oilseed crop with good commercial significance. It is highly variable in phenotypic characters and thus it is important to investigate the variations and associations of these morphological features. Ten confectionary type advanced breeding lines along with two checks (Kadiri chitravathi and Kadir-7) were raised in a randomized block design with three replications and they were evaluated for 15 characters. Significant variations were observed among the genotypes for all the characters studied. The highest genotypic coefficient of variation was observed for hundred pod weight and hundred pod kernel weight indicating the presence of wide range of variation for this character. The dry pod yield per plant had significant positive association with hundred pod kernel weight, kernel yield per plot and positive association with plant height, no. of pods per plant and hundred pod weight. Path coefficient analysis revealed that, hundred pod weight reported the highest positive direct effect on pod yield per plot followed by hundred pod kernel weight, kernel yield per plot, days to maturity, days to 50 % flowering, plant height, final plant count and initial plant count indicating that the selection for these characters was likely to bring about an overall improvement in pod yield per plot directly.

Description of Wickerhamia europaea sp. nov. and revisitation of the ascospore number of W. fluorescens.

During the course of two independent studies, six conspecific yeast strains were recovered from flowers, soil, bird faeces and wood of different geographical origins. The six strains share identical DNA sequences in two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2). According to sequence comparisons and phylogenetic analysis, they represent an undescribed Wickerhamia species. The novel species is not only genetically distinct from W. fluorescens, the single species of the genus but can also be distinguished from it by some phenotypic characters. We propose Wickerhamia europaea sp. nov. (holotype: NCAIM Y.01938; isotype: CBS 18675; MycoBank no.: 856571) to accommodate the above noted strains. Under certain fermentation conditions, we detected the production of phenyllactic acid, a potential broad-spectrum antimicrobial compound against food-borne pathogens, by the type strain of the novel species, although in smaller concentrations than in the case of W. fluorescens. Comparing our observations on the formation and properties of the ascospores of Wickerhamia europaea sp. nov. and the ambiguous data on the number of ascospores per ascus of W. fluorescens, we suggest a possible explanation to reconcile the different data regarding the number of ascospores per ascus formed by W. fluorescens.

Too rough to be a Hypsibius: multipopulation survey accentuates the phylogenetic position and apomorphies of Hypsibius scabropygus (Eutardigrada: Hypsibiidae)

Abstract Tardigrade taxonomy is undergoing a turbulent phase of reclassifying various species that have previously been gathered within large wastebasket genera, such as Diphascon or Hypsibius. The application of genetic sequencing, paired with detailed analysis of fine morphological features in 3D using scanning electron microscopy, allow for revealing new phenotypic characters used in systematics. At the same time, resampling of previously well-sampled regions, such as the Western Palaearctic, delivers fresh and precious data. In this paper, the second from a series of publications integratively addressing the tardigrade fauna of Denmark, we focus on Hypsibius scabropygus and related species, which appeared to be common and abundant in cryptogam samples. As previously suggested by scarce molecular and morphological evidence, Hypsibius scabropygus is considerably different from other representatives of the genus Hypsibius by the presence of ramazzottiid characters. These include Ramazzottius-like claws with thinned, and thus more flexible, primary branches of external/posterior claws, apophyses for the insertion of the stylet muscles asymmetrical with respect to the frontal plane, rudimentary elliptical sensory organs, buccal tube slightly bent in posterior portion, and, finally, eggs with distinct chorion granulation laid in exuviae (known for some hypsibiids and acutuncids), and not smooth, which is otherwise typical for most hypsibiids. Consequently, the group of Hypsibius species with two small granular macroplacoids in the pharynx and pronounced cuticular sculpturing in the form of dorsoposterior protuberances or whole-dorsal tubercles is erected as Parahypsibius gen. nov. New DNA barcodes strongly support the monophyly of Hypsibiidae and recent changes in the classification of Pilatobiinae. We argue that some still poorly resolved nodes in the hypsibiid tree are the result of incomplete representation of particularly uncommon evolutionary lineages. Our abundant cryptogam samples from across Denmark demonstrate the value of involving local communities and utilizing citizen science in biodiversity monitoring and documentation.

Phenotypic Characters and Inheritance Tendency of Agronomic Traits in F1 Progeny of Chinese Cherry

Chinese cherry [Prunus. pseudocerasus Lindl., syn. Cerasus. pseudocerasus (Lindl.) G.Don], an economically important tetraploid fruit crop native to southwestern China, is celebrated as “the earliest fruit of spring”. Understanding the inheritance and heterosis of major agronomical traits is essential for advancing its breeding. In this study, we conducted a three-year observation and inheritance analysis of 32 economic traits in the reciprocal F1 populations (NH, n = 114; HN, n = 87) derived from Chinese cherry landraces “Nanzaohong” and “Hongfei”. The results revealed a broad segregation for all traits in F1 offspring. Fruit size exhibited an inheritance tendency toward smaller dimensions, with some individuals displaying extreme values (Fruit weight, HH = 3.90~12.15%) that highlighted the potential for selecting larger fruits. The hybrids showed a tendency for sweeter fruit flavor, with total soluble solids (RHm = 7.00~19.35%) and soluble sugar (RHm = 11.09% and 17.47%) exhibiting hybrid vigor, along with a decreasing tendency in titratable acid (RHm = −16.08~−1.05%). The flowering and fruiting phenology tended to occur earlier, with extremely early and late flowering lines offering the potential to extend the ornamental and harvesting periods. Fruit bitterness (H2 = 0.98 and 0.95) and fruit skin color (H2 = 0.93 and 0.89) displayed the highest heritability. Correlation analysis revealed strong internal correlations among trait categories, confirming the reliability of the data collection and analysis. Moreover, no significant differences were observed between the maternal and the paternal effect on the inheritance for agronomic traits attributes. This study systematically clarifies the inheritance trends of agronomic traits in Chinese cherry, providing a foundation for the rational selection of parental lines in breeding strategies and laying the groundwork for future molecular genetic research.

Offshoot Decline and Bud Rot of Date Palm Caused by Three Species of Enterobacteriaceae

ABSTRACTDate palm (Phoenix dactylifera) considered a main income and food source for local individuals in producing countries. However, palm offshoot decline and bud rot disease was observed in some palm groves in Khuzestan province as a major date producer in Iran. Thirty‐five samples with rot and decline were collected from diseased offshoot from palm groves of six cities of Khuzestan during 2019–2021. Yellowing in outer leaves, black, brown or reddish brown spots were observed on petioles at the early stage, which gradually continues to rot. Seventy‐nine were isolated from symptomatic samples among which 38 strains caused rotting in the inoculated site and emission of a foul odour 3 weeks after inoculation on petioles and rachises of young offshoots. Based on the phenotypic characters, pathogenic strains categorised in three groups including Klebsiella oxytoca with 15, Kosakonia radicincitans with 12 and Citrobacter koseri with 11 strains. The phylogenic tree based on analysis of the concatenated partial sequences of two housekeeping genes, gyrB and infB, revealed that six representative strains clustered with the type strains of K. oxytoca and K. radicincitans. Furthermore, two strains were clustered with the type strain of C. koseri based on concatenated partial sequences of gyrB, fusA and pyrG genes. This is the first report of K. oxytoca, K. radicincitans and C. koseri, as agents of date palm offshoot decline and bud rot. The inundation of palm groves due to massive flood during 2019 and 2020 in Khuzestan province may intensify the outbreak of decline and offshoot rot disease.

Apothecia trump setae: Paratricharia belongs in the Aulaxina clade and is distant from Tricharia (lichenized Ascomycota: Gomphillaceae)

AbstractThe phylogenetic relationships of the monospecific genus Paratricharia, with the single species P. paradoxa, within the family Gomphillaceae are resolved using newly generated sequences of the mtSSU and nuLSU markers for three specimens collected in Costa Rica. The results support placement as sister to the genus Caleniopsis, the two genera sister to a clade containing the genera Aulaxina and Aulaxinella. This placement confirms earlier studies based on cladistic analysis of phenotype characters and phenotype-based phylogenetic binning, suggesting that apothecial features are more informative for the phylogenetic placement of taxa within Gomphillaceae than thallus characteristics.

Marker Assisted Selection in Advanced Backcross Population of Rice Variety, MTU1010 for Bacterial Blight and Blast Resistance

The present study was aimed for identification of the bacterial blight and blast resistant lines in the advanced back cross population of MTU-1010 using marker assisted foreground selection and also for evaluation of agro-morphological characters. The M-16-59 introgressed line (derived from an intercrossing of BC2F1 plants of MTU-1010 x GPP2 and MTU-1010 x NLR 145) is developed under ongoing DBTDBSRR subproject -IV possessing Xa21, xa13, Pi1 and Pi54 resistance genes having broad spectrum resistance to bacterial blight and blast is used as a donor parent and MTU-1010 was used as a recurrent parent for the back cross. Before attempting the backcross both the parents were verified for the target genes along with the original donors GPP2 and NLR 145 using gene specific/linked molecular markers viz., xa13-promo for xa13 gene, pTA248 for Xa21 gene, RM 224 for Pi1 and Pi54 MAS for Pi54. under the F1 generation (equivalent to BC3F1 because two backcrosses were completed earlier), 120 plants were screened, and 16 plants were confirmed for xa13, Xa21, Pi1, and Pi54 genes under heterozygous conditions. These confirmed plants were assessed for agro-morphological characteristics such as yield, grain features, and plant type. The results showed that the confirmed heterozygous plants were comparable to MTU-1010 and passed to the next round of selection and evaluation. The BC1F1-198th plant (96.8%) was selfed to produce BC1F2 population. Twenty five plants were advanced to BC1F3 generation based on BB resistance and above other phenotypic characters. The selected BC1F3 progenies were screened for blast and BB resistance. Four BC1F3 progenies with four target genes (xa13xa13Xa21Xa21Pi54Pi54Pi1Pi1) showed very high level of resistance to both the diseases. BC1F2-198-52nd line found similar to MTU1010 with respect to yield and yield related characters besides showing resistance to both BB and blast.Improved lines of MTU1010 can be advanced for multi-location testing under All India Coordinated Rice Improvement Project (AICRIP) for their evaluation and possible release for the benefit of rice farmers.

Advanced Plant Phenotyping: Unmanned Aerial Vehicle Remote Sensing and CimageA Software Technology for Precision Crop Growth Monitoring

In production activities and breeding programs, large-scale investigations of crop high-throughput phenotype information are needed to help improve management and decision-making. The development of UAV (unmanned aerial vehicle) remote sensing technology provides a new means for the large-scale, efficient, and accurate acquisition of crop phenotypes, but its practical application and popularization are hindered due to the complicated data processing required. To date, there is no automated system that can utilize the canopy images acquired through UAV to conduct a phenotypic character analysis. To address this bottleneck, we developed a new scalable software called CimageA. CimageA uses crop canopy images obtained by UAV as materials. It can combine machine vision technology and machine learning technology to conduct the high-throughput processing and phenotyping of crop remote sensing data. First, zoning tools are applied to draw an area-of-interest (AOI). Then, CimageA can rapidly extract vital remote sensing information such as the color, texture, and spectrum of the crop canopy in the plots. In addition, we developed data analysis modules that estimate and quantify related phenotypes (such as leaf area index, canopy coverage, and plant height) by analyzing the association between measured crop phenotypes and CimageA-derived remote sensing eigenvalues. Through a series of experiments, we confirmed that CimageA performs well in extracting high-throughput remote sensing information regarding crops, and verified the reliability of retrieving LAI (R2 = 0.796) and estimating plant height (R2 = 0.989) and planting area using CimageA. In short, CimageA is an efficient and non-destructive tool for crop phenotype analysis, which is of great value for monitoring crop growth and guiding breeding decisions.

Phenotypes of occupational bronchial asthma from the standpoint of immunopathogenesis

IIntroduction. Currently, occupational bronchial asthma is considered as a phe notypically and genetically heterogeneous disease. The assessment of clinical data, func tional features, and immunopathogenesis opens up new opportunities in assessing the development, predicting the characteristics of the course, and working out a personalized approach to pharmacotherapy of occupational asthma, as well as in developing an individ ual strategy for its prevention. The purpose of the study was to determine clinical and immunological markers of the risk of developing occupational asthma under conditions of exposure to sensitizing substances in various phenotypes of this disease. Materials and methods. The study included 170 patients with various OA phenotypes and 50 participants in the control group. The pulmonary function test was carried out on the CareFusion MicroLab Desktop Spirometer (Great Britain). The levels of IL-17, TNF-α, vas cular endothelial growth factor (VEGF), MCP-1, IFN-γ, and total IgE in blood serum were determined by solid-phase enzyme immunoassay using kits and reagents (OOO «Protein contour», «Vector-Best», «Diatex-E», «DIA-plus», «Pharmacia diagnostika»). Results. For the first time, the features of clinical and immunological manifestations in allergic and non-allergic OA phenotypes, as well as phenotypes of OA combination with occupational chronic obstructive pulmonary disease and metabolic syndrome were es tablished; the features of formation, immunopathogenesis, and prognosis in various phe notypes of occupational bronchial asthma were revealed. This allows recommending the determination of these immunological parameters during in-depth periodic medical exam inations of workers under conditions of exposure to sensitizing and irritating substances for differential diagnosis of various phenotypes of occupational bronchial asthma in a specialized inpatient examination. Limitations of the study. The study has regional (Samara region) and professional (in terms of detailing the working conditions in the studied comparison groups) limitations. Conclusion. The identified clinical, immunological, and genotypic features in various OA phenotypes and the established profiles of OA genotypes can optimize the approach to early diagnosis, prognosis, prevention, and pharmacotherapy of this disease, as well as expand the list of immunological study indicators used during preliminary and periodic medical examinations, in-depth examination of patients with occupational bronchial asth ma in occupational disease clinics and occupational pathology centers, and the application of new reliable criteria for predicting the course of the disease.

Geographical variation and genetic diversity of Parashorea chinensis germplasm resources.

Parashorea chinensis is a rare monodominant species in southwest China known for its production of high-quality timber, is facing decline due to its narrow distribution, human interference and habitat destruction. However, there are no reports on genetic diversity and geographical variation of phenotypic traits of P. chinensis. In this study, phenotypic characters and genetic diversity of 15 germplasms resources from five provenances in southwest China were investigated, and their relationships with geographical and environmental factors was discussed. Our results revealed a rich phenotypic diversity among the germplasms, with variation coefficients ranging from 3.63% to 45.49%. Among the studied germplasms, NP03 from Napo and ML02 from Mengla region exhibited superior phenotypic traits. Notably, NP03 also demonstrated the highest genetic diversity. Genetic differentiation analyses including genetic differentiation coefficient (0.6264) and gene flow (0.3736) illustrated that genetic variation was most prevalent among populations. Furthermore, redundancy analysis showed that temperature related factors (maximum air temperature, annual mean temperature and minimum air temperature) significantly affected phenotypic variation. Similarly, altitude, longitude, latitude, annual mean precipitation and the minimum air temperature significantly impacted the level of genetic diversity. The molecular variation of the natural population of P. chinensis followed a certain geographical pattern. Our finding indicated abundant phenotypic variation among P. chinensis germplasms. However, populations exhibited low levels of genetic diversity alongside high genetic differentiation, potentially contributing to the species' rarity. Based on our results, NP03 and ML02 germplasm could be used as the parents for breeding superior germplasm of P. chinensis. Overall, this study provides valuable insights into germplasm diversity and conservation, genetic improvement, and utilization of P. chinensis.

New emerging Pseudomonads as causal agents of bean blight disease

Common bean (Phaseolus vulgaris) production is negatively affected by several bacterial plant diseases. A severe outbreak of bean blight was observed in the nine major bean-producing provinces of Iran during 2021–2022. Necrotic spots were observed on leaves which become necrotic with chlorosis beyond it. One hundred-sixty bacterial strains with a greyish-white colony appearance were consistently isolated from the one-hundred eighteen symptomatic bean leaf, pod, seed and root samples on nutrient agar. All strains were screened for their ability to cause disease bean leaves among which 134 strains induced chlorosis three days after inoculation on bean leaves of cv. Yaghoot followed by necrotic spots on the inoculated sites one week after inoculation. The pathogenic strains clustered in three groups based on phenotypic characters and multilocus sequencing analyses. Three housekeeping genes including gyrB, rpoB, and rpoD of representative strains were partially sequenced. In the phylogenetic tree based on concatenated sequences of these three genes or each gene individually, the strains were divided into three clusters each with high bootstrap support. The first group of the strains clustered with Pseudomonas simiae CCUG 50988T. This is the first report of this species as causal agent of bean blight. The second group clustered close to Pseudomonas alloputida NMI5768T which apparently belong to a new species. The third group clustered in a separate clade in Pseudomonas chlororaphis species which belongs to a new subspecies based on pathogenicity on bean, phenotypic characters, sequences of five housekeeping genes which named as subsp. phaseoli subsp. nov. with the type strain UT-M315.

Multi-gene phylogeny and phenotypic analyses revealed an association of different Colletotrichum species with inflorescence dieback and leaf spot of arecanut in India

Arecanut is one of the economically important plantation crops. Among the various diseases, inflorescence dieback and leaf spot/blight diseases caused by Colletotrichum spp. have re-emerged as major factors impeding arecanut production in India in the last few years. To understand the Colletotrichum species complex in the arecanut system, we have characterized Colletotrichum spp. associated with inflorescence dieback and leaf spot/blight of arecanut based on a combination of phenotypic, multi-locus (ITS, ACT, CHS-1, GAPDH, HIS3 and TUB2) phylogeny and pathogenicity studies. A total of 26 Colletotrichum isolates were obtained from arecanut inflorescence dieback (13 isolates) and leaf spot/blight (13 isolates) infected tissues collected from disease-endemic regions of Karnataka, Kerala and Tripura states of India. The combined multi-locus sequence analyses and a critical examination of phenotypic characters revealed the association of Colletotrichum aoteaora as a dominant species with arecanut inflorescence dieback disease. On the other hand, two Colletotrichum species, viz., C. siamense and C. fructicola, were distinctly associated with leaf spot/blight disease. All the Colletotrichum isolates studied were pathogenic to arecanut. Significant variations in lesion size were observed among the different species with cross-infection ability on inflorescence and leaves. This study represents the first comprehensive study of Colletotrichum spp. associated with arecanut inflorescence dieback and leaf spot/blight diseases. In addition, the study is the first record of C. aoteaora, C. siamense, and C. fructicola associated with the arecanut crop in this country. It provides valuable information for implementing effective IDM strategies against these diseases in India.

Mitonuclear and phenotypic discordance in an Atlantic Forest frog hybrid zone.

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic-scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species.

Chemotaxonomic and molecular phylogenetic studies of selected Hypoxylon species from the Neotropics

ABSTRACT Members of the genus Hypoxylon (Ascomycota) are pleomorphic fungi mostly forming conspicuous teleomorphs, consisting of perithecia embedded into stromal tissue, and their morphology has traditionally served for species delineation. However, analysis in tandem with other phenotypic characters, such as chemical and genetic traits, proved to be a more stable predictor of interspecies and intergeneric relationships. During 2014 and 2015, a set of species identified as Hypoxylon were described from the Neotropics, exclusively relying on morphological traits. The secondary metabolite profiles of their stromata were analysed by HPLC/DAD-ESI-MS, corroborating their classification within Xylariales. Additionally, molecular data for ex-type strains of H. dussii and H. sofaiense were incorporated into an inferred molecular phylogeny of the Hypoxylaceae and allies. Furthermore, a freshly collected specimen from North Carolina was selected as epitype of Sphaeria perforata Schweinitz (syn. Hypoxylon perforatum), as its morphological/chemotaxonomic characters matched those of the holotype. Our findings demonstrate that the secondary metabolism of Hypoxylon closely correlates with both morphological features and molecular data, serving as a complement for species identification.

Phenotypic and Molecular-Markers-Based Assessment of Jamun (Syzygium cumini) Genotypes from Pakistan

Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs.

Femoral diversity in titanosaur sauropods from the Villalba de la Sierra Fm. (Central Spain): Implications for the characterization of faunal turnover in the Ibero-Armorican Late Cretaceous

The late Campanian-Maastrichtian in the Ibero-Armorican domain is rich in titanosaurian fossils. The sauropod remains exhibit a high degree of morphological variability, especially in the commonly-found appendicular elements. The phylogenetic relationships of the Ibero-Armorican titanosaurs are still uncertain but we do know that they experienced a Campanian-Maastrichtian herbivorous faunal turnover. It is probable that the small-to-medium-sized Lirainosaurinae-dominated faunas of the Campanian were replaced by late–early Maastrichtian large-bodied lithostrotian dominated faunas. In this context, the Villalba de La Sierra Formation has yielded an abundant sample of medium-to-large sized titanosaurs. In this study we analyze the morphological variability in the appendicular skeleton of the titanosaurs from the Campanian-Maastrichtian Ibero-Armorican domain. We follow previous attempts to classify the commonly-found isolated titanosaurian femora and expand the proposed methodology. The use of combined phenotypic characters and linear morphometrics can be helpful to analyze the morphological variability and diversity of the Ibero-Armorican titanosaurs. Our findings corroborate the presence of at least two exclusive morphotypes in the Lo Hueco fossil site and one exclusive morphotype in the Poyos site, as well as the presence of previously defined Lirainosaurinae across the Pyrenees during the Campanian-Maastrichtian. The Villalba de La Sierra Formation titanosaurs are also clustered with large-bodied late Maastrichtian titanosaurs. It is possible that either the large-bodied late–early Maastrichtian immigrants, with possible Gondwanan affinities, entered the Iberian Peninsula much earlier or that this group was already present at least during the Campanian-Maastrichtian transition, as the small-sized Lirainosaurinae declined.

Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp

Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.

In vitro Propagation of <i>Citrus aurantifolia</i> and its Conservation in Pakistan

Citrus varieties are propagated by both asexual and sexual methods. Generally, rootstocks are propagated sexually through seeds, while most of the commercial varieties are propagated by various asexual methods such as grafting and budding. The technology called plant tissue culture is used for commercial production of plants that are microbe and virus free and to save germplasm of infrequent or threatened species of plants. Fast reproduction techniques have the potential to produce plants free of viruses. Likewise, traditional propagation methods are old, time consuming and are difficult. Tissue culture techniques are assumed for reliable commercial production of economically important plants. In present study shoot tips of Citrus aurantifolia were collected from the field of BCI, NARC. Different disinfectant (Ethanol and NaOCl) with the concentration ranging from 10 to 20 percent were used for culture establishment. Maximum survival percentage was observed in 10% NaOCl. After 5 weeks, established cultures were shifted to hormonal growth media (BAP, GA3 and NAA) at the concentration ranging from 0.1 to 0.8 mg/L. Our finding results that maximum phenotypic characters (plant height, number of leaves and number of shoots were observed on BAP at the concentration of 0.1 to 0.3 mg/L, while maximum number of roots were observed on NAA at the concentration of 0.5mg/L. In present study, for in vitro conservation different conservants like sorbitol and mannitol (10, 20 and 30 g/L) were used. Incubation of cultures was maintained at 21°C under the light intensity of 1000 lux. Old cultures of Citrus aurantifolia were shifted in conservant media. Overall, remarkable difference was observed. In present study mannitol at the concentration of (10, 20 and 30 g/L) showed slow growth after 35 days. In future the plants in conservation media will be used for further propagation and for growing them in fields.

Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers.

Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.