Phylogenetic Principal Component Analysis Research Articles

Traits associated with the conservation gradient are the strongest predictors of early‐stage fine root decomposition rates

Abstract Fine root traits span two independent axes of variation, the conservation and collaboration axes, which define the root economic space (RES). However, whether early‐stage fine root decomposition rates (quantified as proportion mass loss, i.e. pml) are more strongly related to collaboration or conservation traits remains unclear. We studied 63 tree species in New Zealand's temperate rain forest. We determined the phylogenetic signal in pml and fine root traits, conducted phylogenetic principal component analysis and used phylogenetic generalized least squares to determine which traits are most strongly related to pml. Root decomposition exhibited a high phylogenetic signal and was more strongly related to the conservation than the collaboration axis. Root tissue density (RTD) was negatively correlated and root nitrogen (RN) was positively correlated with pml. Root diameter was positively yet weakly correlated with pml, but specific root length was uncorrelated with pml. The lignin‐to‐N ratio and root cellulose were the strongest predictors of pml. Synthesis: Early‐stage fine root decomposition is most strongly driven by tissue quality traits, such as root nitrogen, tissue density and lignin‐to‐N ratio, which all align with the conservation axis of the root economics space. However, root diameter plays a weak yet undeniable role in early‐stage fine root decomposition. Some thick‐rooted species decomposed faster, possibly due to the higher quality cortical tissue. Thin‐rooted species decomposed slower, possibly because of their higher cellulose concentration that maintains the structural integrity of small diameter roots. Relationships between decomposition and other traits that align with the collaboration gradient deserve further study across the phylogeny of vascular plants.

Population structure of the B0/W148 Mycobacterium tuberculosis subtype: Phylogenetic analysis and characteristics of genotypic drug resistance

Background. The B0/W148 subtype belongs to the L2phylogenetic lineage of Mycobacterium tuberculosis and is most common in the former Soviet Union. Test systems capable of detecting genetic variants of the pathogen are needed for effective epidemiological surveillance. Studying the genetic diversity of B0/W148 strains and finding molecular markers suitable for their genotyping are key steps in the development of such diagnostic tools.The aim of the work. To study the phylogenetic diversity of the B0/W148 subtype circulating in the territory of the Russian Federation and neighboring countries in order to identify unique clades and search for specific molecular markers suitable for their precise identification.Materials and methods. The study used DNA samples of B0/W148 strains (n = 34) isolated in different regions of the Russian Federation, as well as genomic data obtained from the SRA NCBI (Sequence Read Archive of the National Center for Biotechnology Information) (n = 419). Phylogenetic analysis and principal component analysis (PCA) of whole genome sequencing (WGS) data were used to analyze genetic diversity and to identify molecular markers. An evolutionary reconstruction of the age of the identified clades was carried out.Results. The analysis of the B0/W148 genomes (n = 453) revealed that they are divided into three phylogenetic clades: B – basal, M – minor and P – principal. It was found that specific mutations in the M and P clades allow for their differential diagnosis. The 4137219T>G mutation is unique for the M clade, and the 2241091C>T mutation is unique for the P clade. No characteristic mutations were found among the strains of B clade. In addition, unique mutation profiles in the genes responsible for drug resistance were identified for the clades.Conclusion. The study showed that B0/W148 strains represent a genetically heterogeneous population divided into B, M and P clades. M and P Clades have unique mutations that allow for their identification. It was also found that all clades are characterized by the presence of specific mutation profiles in drug resistance genes.

Population data for 12 X-STRs loci in Malaysian Malay and Chinese populations

The utilization of X-chromosome short tandem repeats (X-STRs) for human identification particularly in resolving complex kinship cases has been advocated. Since, forensic statistical parameters vary among different populations, and because the X-STRs population data representing the diverse population of Peninsular Malaysia remain unavailable, the specific attempt reported here for the Malays (n = 224) and Chinese (n = 201) populations appears forensically relevant to support the evidential value of the 12 X-STRs markers for human identification in Malaysia. Results derived from the Qiagen Investigator® Argus X-12 kit revealed that DXS10135 as the most polymorphic locus with high genetic diversity, polymorphic information content, heterozygosity as well as power of exclusion. Based on allele frequencies, the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) values for the Malays and Chinese were individually ≥0.999995532964908. As for the combined power of discrimination as well as the mean exclusion chance (MECKrüger, MECKishida, MECDesmarais and MECDesmaraisDuo) calculated based on haplotype frequencies, the values were ≥0.9999986410567 for the Malays and Chinese populations. In addition, results from the genetic distance, neighbor-joining phylogenetic tree and principal component analysis revealed close biogeographical distributions of the studied populations with other South East Asian populations. Hence, the utilization of the X-STRs data for identifying individuals among the Malays and Chinese populations in Peninsular Malaysia for forensic application appears as highly supported.

Generic Workflow of a Highly Effective and Easy Anther Culture Method for Both Japonica and Indica Rice.

As one of the most important staple crops in the world, rice plays a pivotal role in world food security. The creation of doubled haploids based on anther culture is an important technology for rice breeding. However, at present, rice anther culture technology still faces many problems, such as genotype dependency, especially genotypes of indica rice. In this study, fifteen rice genotypes, including twelve japonica rice genotypes and three indica rice genotypes, were randomly selected and used to study anther culture by using a modified M8 medium. The results showed that the total callus induction rates of these different rice genotypes ranged from 0.81 to 13.95%, with an average of 6.64%, while the callus induction rates calculated for the top ten highest callus inductions for each rice genotype ranged from 2.75 to 17.00%, with an average of 10.56%. There were varying gaps between the total callus induction rates and the callus induction rates in these different rice genotypes. The fact that the gaps for some rice genotypes were relatively large indicated that standard tiller or anther collection was not applicable to all rice genotypes and that there was still a lot of room for improvement in the callus induction rate of some rice genotypes through optimization of the sampling method. The plantlet regeneration rates ranged from 12.55 to 456.54%, with an average of 200.10%. Although there were many albinos from anther culture for some rice genotypes, these would still meet the requirement if the rice genotypes had higher callus induction rates or regeneration rates. The percentages of seed setting of regenerated green seedlings ranged from 14% to 84%, with an average of 48.73%. Genetic diversity analysis showed that the genetic background of these different rice genotypes was representative, and the phylogenetic tree and Principal Component Analysis (PCA) divided them into indica and japonica types. Therefore, in this study, an anther culture method suitable for both indica and japonica rice genotypes was established, which could improve doubled haploid breeding in rice.

BIOINFORMATICS AND MOLECULAR ANALYSES IDENTIFIED THE CONTROL REGION AS THE MOST POWERFUL MITOGENOMIC MARKER FOR DISTINGUISHING THE MAIN MATERNAL HAPLOGROUPS IN GOATS

Identification of genetic markers to distinguish animals within and between species demands extensive genomic and bioinformatics investigation. Previous studies have not carefully taken into consideration the effect of mitogenomic components on the genetic differentiation of the maternal lineages in goats. As a precaution, the complete goat mitogenome was downloaded from the NCBI database and used in the current study to assess the effects of the choice of mitogenomic fragments on phylogenetic studies and to identify any potential polymorphic region by which the main maternal haplogroups of goats can be classified. Phylogenetic results confirmed that all 13 individual mitochondrial protein-coding genes and 2 ribosomal genes are not applicable to differentiate the maternal lineages. Instead, a single novel polymorphic region with a length of 756 bp within the control region was successfully amplified by newly designed primers. Both phylogenetic analysis and principal components analysis of the sequenced mitogenomic region of the mtDNA control region efficiently differentiated the main maternal haplogroups in goats. Higher numbers of polymorphic sites were found in the control region and the mitogenomic marker region. Highly significant correlations were discovered between the polymorphic sites and the length of each individual mitogenomic component. Our results demonstrate useful guidance and cautionary notes for researchers who are interested in the investigation of genetic diversity in animal species using mtDNA sequences. The bioinformatics and molecular methods used herein can be powerful in selecting a minimum amount of data using PCR amplification when the entire sequences of the mitogenome are unavailable.

Gymnosperms demonstrate patterns of fine‐root trait coordination consistent with the global root economics space

Abstract Gymnosperms encompass a diverse group of mostly woody plants with high ecological and economic value, yet little is known about the scope and organization of fine‐root trait diversity among gymnosperms due to the undersampling of most gymnosperm families and the dominance of angiosperm groups in recent syntheses. New and existing data were compiled for morphological traits (root diameter, length, tissue density, specific root length [SRL] and specific root area [SRA]), the architectural trait branching ratio, root nitrogen content [N] and mycorrhizal colonization. We used phylogenetic least squares regression and principal component analysis to determine trait–trait relationships and coordination across 66 species, representing 11 of the 12 extant gymnosperm families from boreal, temperate, subtropical and tropical biomes. Finally, we compared the relationship between family divergence time and mean trait values to determine whether evolutionary history structured variation in fine‐root traits within the gymnosperm phylogeny. Wide variation in gymnosperm root traits could be largely captured by two primary axes of variation defined by SRL and diameter, and root tissue density and root nitrogen, respectively. However, individual root length and SRA each had significant correlations with traits defining both main axes of variation. Neither mycorrhizal colonization nor root branching ratio were closely related to other traits. We did not observe a directional evolution of mean trait values from older to more recently diverged gymnosperm families. Synthesis. Despite their unique evolutionary history, gymnosperms display a root economic space similar to that identified in angiosperms, likely reflecting common constraints on plants adapting to diverse environments in both groups. These findings provide greater confidence that patterns observed in broad syntheses justly capture patterns of trait diversity among multiple, distinct lineages. Additionally, independence between root architecture and other traits may support greater diversity in below‐ground resource acquisition strategies. Unlike angiosperms, there were no clear trends towards increasingly thin roots over evolutionary time, possibly because of lower diversification rates or unique biogeographic history among gymnosperms, though additional observations are needed to more richly test evolutionary trends among gymnosperms.

Forensic parameters and population analysis of 21 autosomal STR loci in the Wuhu Han population from Anhui Province, East China

Background At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. Aim This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. Subjects and methods Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. Results In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni’s correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. Conclusion The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.

Analytical advances alleviate model misspecification in non-Brownian multivariate comparative methods.

Adams and Collyer argue that contemporary multivariate (Gaussian) phylogenetic comparative methods are prone to favouring more complex models of evolution and sometimes rotation invariance can be an issue. Here we dissect the concept of rotation invariance and point out that, depending on the understanding, this can be an issue with any method that relies on numerical instead of analytical estimation approaches. We relate this to the ongoing discussion concerning phylogenetic principal component analysis. Contrary to what Adams and Collyer found, we do not observe a bias against the simpler Brownian motion process in simulations when we use the new, improved, likelihood evaluation algorithm employed by mvSLOUCH, which allows for studying much larger phylogenies and more complex model setups.

Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat.

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.

Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability

Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.

Population genetic structure and implication for adaptive differentiation of the snail (Gastropoda, Provannidae) in deep‐sea chemosynthetic ecosystems

AbstractThe snail Provanna glabra is a dominant species inhabiting both hydrothermal vents and cold seeps of the Northwest Pacific Ocean. The genetic diversity and population structure of the snail from the hydrothermal vents of Okinawa Trough and a methane seep in the South China Sea were investigated using mitochondrial cytochrome c oxidase subunit I (COI) and genome‐wide single nucleotide polymorphisms (SNPs). A total of 28,805 SNPs were screened based on 2b‐RAD sequencing. Substantial genetic differences between vent and seep populations were identified based on the two datasets with FST = 0.753 (COI) and FST = 0.109 (SNPs), respectively. The results of phylogenetic tree, ADMIXTURE and principal component analysis jointly supported the population differentiation. Outlier detection confirmed the local adaptation of P. glabras populations, and the annotation of these outliers revealed that they were closely associated with processes of signal transduction, immunity, DNA repair, transposable elements and biological development. The genetic divergence observed between hydrothermal vent and methane seep P. glabra populations might be induced by the geographic barrier, limited dispersal ability and natural selection imposed by local environmental pressures from different deep‐sea habitats, e.g. chemical composition, temperature and microbes. These results provide a genetic basis for the microevolution of snails inhabiting deep‐sea chemosynthetic ecosystems.

Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce.

Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs. In this work, we report the design and application of the first SPET panel in lettuce, consisting of 41,547 probes spanning the whole genome and designed to target both coding (~96%) and intergenic (~4%) regions. A total of 81,531 SNPs were surveyed in 160 lettuce accessions originating from a total of 10 countries in Europe, America, and Asia and representing 10 horticultural types. Model ancestry population structure clearly separated the cultivated accessions (Lactuca sativa) from accessions of its presumed wild progenitor (L. serriola), revealing a total of six genetic subgroups that reflected a differentiation based on cultivar typology. Phylogenetic relationships and principal component analysis revealed a clustering of butterhead types and a general differentiation between germplasm originating from Western and Eastern Europe. To determine the potentiality of SPET for gene discovery, we performed genome-wide association analysis for main agricultural traits in L. sativa using six models (GLM naive, MLM, MLMM, CMLM, FarmCPU, and BLINK) to compare their strength and power for association detection. Robust associations were detected for seed color on chromosome 7 at 50 Mbp. Colocalization of association signals was found for outer leaf color and leaf anthocyanin content on chromosome 9 at 152 Mbp and on chromosome 5 at 86 Mbp. The association for bolting time was detected with the GLM, BLINK, and FarmCPU models on chromosome 7 at 164 Mbp. Associations were detected in chromosomal regions previously reported to harbor candidate genes for these traits, thus confirming the effectiveness of SPET for GWAS. Our findings illustrated the strength of SPET for discovering thousands of variable sites toward the dissection of the genomic diversity of germplasm collections, thus allowing a better characterization of lettuce collections.

The mycoremediation potential of the armillarioids: a comparative genomics analysis.

Genes involved in mycoremediation were identified by comparative genomics analysis in 10 armillarioid species and selected groups of white-rot Basidiomycota (14) and soft-rot Ascomycota (12) species to confine the distinctive bioremediation capabilities of the armillarioids. The genomes were explored using phylogenetic principal component analysis (pPCA), searching for genes already documented in a biocatalysis/biodegradation database. The results underlined a distinct, increased potential of aromatics-degrading genes/enzymes in armillarioids, with particular emphasis on a high copy number and diverse spectrum of benzoate 4-monooxygenase [EC:1.14.14.92] homologs. In addition, other enzymes involved in the degradation of various monocyclic aromatics were more abundant in the armillarioids than in the other white-rot basidiomycetes, and enzymes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) were more prevailing in armillarioids and other white-rot species than in soft-rot Ascomycetes. Transcriptome profiling of A. ostoyae and A. borealis isolates confirmed that several genes involved in the degradation of benzoates and other monocyclic aromatics were distinctively expressed in the wood-invading fungal mycelia. Data were consistent with armillarioid species offering a more powerful potential in degrading aromatics. Our results provide a reliable, practical solution for screening the likely fungal candidates for their full biodegradation potential, applicability, and possible specialization based on their genomics data.

Population genetic assessment of Viburnum japonicum in China using ddRAD-seq.

Viburnum japonicum is a rare plant species and endemic to the coastal region of Eastern Asia with extremely small populations. Within mainland China, this species can be only found in narrow habitats of the northeast coastal islands of Zhejiang Province. However, there are scarce conservation genetic studies on V. japonicum, which has limited the effective conservation and management of this rare species. Here, 51 individuals in four natural populations covering the Chinese geographic range of the species were sampled to assess the genetic diversity and population structure. A total of 445,060 high-quality single nucleotide polymorphisms (SNPs) were identified using double digest restriction-site associated sequencing (ddRAD-seq). The overall average values of observed heterozygosity (Ho), expected heterozygosity (He), and average nucleotide diversity (π), were 0.2207, 0.2595, and 0.2741, respectively. The DFS-2 population exhibited the highest level of genetic diversity among all the populations. Genetic differentiation between populations was moderate (F ST = 0.1425), and there was selfing between populations (F IS = 0.1390, S = 24.52%). Of the total genetic variation, 52.9% was found among populations through AMOVA analysis. The Mantel test (r = 0.982, p = 0.030) combined with analyses of the Maximum Likelihood (ML) phylogenetic tree, ADMIXTURE, and principal component analysis (PCA), revealed that populations of V. japonicum were genetically segregated and significantly correlated with their geographical distribution. Our study demonstrated that V. japonicum maintained a medium level of genetic diversity and differentiation with a strong population structure, and the results were mainly affected by its island distribution pattern and self-crossing characteristics. These results provide insights into the genetic diversity and population history of V. japonicum, critical information for conserving and sustainably developing its genetic resources.

Molecular marker development and genetic diversity exploration in Medicago polymorpha.

Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding.

Population whole-genome resequencing reveals the phylogenetic relationships and population structure of four Hunan typical tea landraces

Hunan located at the evolutionary transitional zone edge of the Yunnan-Guizhou plateau, tea germplasms are abundant. At present, although morphological, enzymological and molecular markers have been used to study the genetic relationship of these tea germplasms. However, due to the complexity of the genetic background of tea germplasm resources, the evolution history and taxonomy of Hunan tea germplasm is still unclear. In this study, four Hunan tea landraces from the evolutionary transitional zone were collected, including 9 'Chengbu Dongcha' (CBDC), 8 'Jianghua Kucha' (JHKC), 11 'Rucheng Baimao' (RCBM) and 8 'Anhua Yuntai' (AHYT). We used whole-genome re-sequencing to identify genetic variation, phylogenetic placement, and population structure among the four tea landraces and then scanned the genome for regions related to population potential selective. Across the samples, we identified an average of 1.38 million (M) SNPs and 6.82 × 10³ INDELs. Based on the high-quality SNPs, we performed neighbor-joining phylogenetic tree, population structure, and principal component analysis, all of which supported that the 36 tea germplasms could been divided into two groups, CBDC and AHYT were clustered into a group, and RCBM and JHKC were clustered into another group. With CBDC, JHKC, and RCBM as control, 407, 380, and 147 selected genes were identified in AHYT, respectively, were in the top 5% of F_ST and Log₂^Ratioθπ scores. The identified genes are mainly involved in stress tolerance, biosynthesis of important secondary metabolites, adaptability, and yield. These results will be helpful in the classification of tea germplasms and investigating selection–related genes.

SLAF-Seq Technology-Based Genome-Wide Association and Population Structure Analyses of Ancient Camellia sinensis (L.) Kuntze in Sandu County, China

Guizhou is one of the centers of origin for the tea plant (Camellia sinensis (L.) Kuntze). The location contains highly diverse ancient tea plant germplasms in its Sandu Aquarium Autonomous County. After a prolonged course of continuous evolution, these ancient plants have gained a wealth of genetic diversity. Their resources could be harnessed for the selection and breeding of fine varieties of tea plant, as well as for the effective utilization and protection of germplasm resources. In this study, the specific locus-amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) for the three traits of 125 ancient tea plants in the Sandu County of Guizhou province, China. A total of 807,743 SLAF tags and 9,428,309 population single-nucleotide polymorphism (SNP) tags were obtained. The results of the phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 125 germplasms were clustered into four groups, and the heterozygosity rates for groups I, II, III, and IV, were 0.211, 0.504, 0.144, and 0.192, respectively. Additionally, GWAS analysis suggested that seven candidate genes were related to altitude at the origin of the plants, eight were related to tree shape, and three were associated with leaf color. In this study, we clarified genetic relationships between four ancient tea plant-producing areas in Sandu County and obtained candidate genes related to their development associated with altitude, tree shape, and leaf color. The study provides useful information for tea plant-breeding development and molecular identification.

Morphometric analysis of the elasmobranch olfactory rosette.

The olfactory rosettes of elasmobranchs vary in shape and structure among species, but the functional consequences of this diversity are unresolved. Our goal was to quantify rosette morphology on dissected as well as diffusible iodine-based contrast-enhanced computed tomography (diceCT)-imaged specimens to analyze the drivers of observed trends in a phylogenetic context and compare the methodologies. We hypothesized that lamellar count and rosette shape (fineness ratio) would not scale with animal size, but other rosette size variables would scale positively. We dissected rosettes from 14 elasmobranch species and collected morphometric data (fineness ratio, lamellar count, interlamellar distance, lamellar thickness, and raphe width). A subset of rosettes (five species) wasused to analyze the effects of body size, while all 14 species were used for a phylogenetic principal component analysis (pPCA). We found that fineness ratio and lamellar counts varied significantly among species, and were positively correlated. The first two principal components of the pPCA explained 82% of the variation, with fineness ratio and lamellar count contributing most to the loadings, respectively.DiceCTwas used for in situ imaging of four species of Carcharhiniformes. There were no significant differences between rosette structure or volume when comparing values from dissected specimens to values from in situ specimens obtained using diceCT. We also quantified the volume of the excurrent channel in the olfactory capsule. These data add to our understanding of how olfactory organ shape varies among species and can be used to create three-dimensional models for future olfactory hydrodynamic studies.

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count.

Simple SummaryChinese Holstein cows, crossbred cattle in China, have abundant genetic diversity due to the fact that Holstein cows were crossbred with various local breeds. Therefore, to reveal their genetic diversity, we sequenced the complete mitochondrial DNA (mtDNA) D-loop region of 501 Chinese Holstein cows and found abundant genetic resources (including 219 haplotypes, polymorphisms of 260 SNPs, and 32 indels) and two haplogroups in the study population. Meanwhile, the two haplogroups had different maternal origins and corresponding distinguished mutations. Furthermore, the association between haplogroups and antral follicle count was found, and the mtDNA haplogroup HG1 with Bos indicus maternal origin had more antral follicles (diameter ≥ 8 mm), implying that these individuals of HG1 had higher reproductive potential. Finally, these distinguished mutations between two haplogroups could be considered as important genetic markers for cattle breeding.Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.

Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae).

Species of Osmanthus are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) have rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated the: “Caucasian Osmanthus” (corresponding to O. decorus), “Siphosmanthus” (corresponding to O. sect. Siphosmanthus), “O. serrulatus + O. yunnanensis,” and “Core Osmanthus: (corresponding to O. sect. Osmanthus + O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus Osmanthus at 12.66 Ma; “Siphosmanthus” clade at 5.85 Ma; “O. serrulatus + O. yunnanensis” at 4.89 Ma; and “Core Osmanthus: clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of Osmanthus were spring flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring‐flowering species from autumn‐flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.