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Understanding the molecular associations underlying pathogen resistance in invasive plant species is likely to provide useful insights into the effective control of alien plants, thereby facilitating the conservation of native biodiversity. In the current study, we investigated pathogen resistance in an invasive clonal plant, Sphagneticola trilobata, at the molecular level. Sphagneticola trilobata (i.e., Singapore daisy) is a noxious weed that affects both terrestrial and aquatic ecosystems, and is less affected by pathogens in the wild than co-occurring native species. We used Illumina sequencing to investigate the transcriptome of S. trilobata following infection by a globally distributed generalist pathogen (Rhizoctonia solani). RNA was extracted from leaves of inoculated and un-inoculated control plants, and a draft transcriptome of S. trilobata was generated to examine the molecular response of this species following infection. We obtained a total of 49,961,014 (94.3%) clean reads for control (un-inoculated plants) and 54,182,844 (94.5%) for the infected treatment (inoculated with R. solani). Our analyses facilitated the discovery of 117,768 de novo assembled contigs and 78,916 unigenes. Of these, we identified 3506 differentially expressed genes and 60 hormones associated with pathogen resistance. Numerous genes, including candidate genes, were associated with plant-pathogen interactions and stress response in S. trilobata. Many recognitions, signaling, and defense genes were differentially regulated between treatments, which were confirmed by qRT-PCR. Overall, our findings improve our understanding of the genes and molecular associations involved in plant defense of a rapidly spreading invasive clonal weed, and serve as a valuable resource for further work on mechanism of disease resistance and managing invasive plants.

Relatively large number of bitter melon microsatellite markers have been reported; however, only few resulted in successful PCR amplification and a small fraction shown polymorphisms. This limited chance of recovering polymorphic markers makes the primer screening a cost-demanding process. To test the hypothesis that microsatellites with longer motifs as well as shorter motifs repeated substantially shall have better prospects to be polymorphic, we performed a genome-wide microsatellite mining. We selected a sample of genome-wide microsatellites with prescribed motif lengths or satisfying a target repeat number, which were considered potentially-hyper variable, for primer designing and validation. Seventy five microsatellites satisfying these criteria were identified, of which 69 were validated through successful PCR amplification. Among them, 40 (53.33% of the markers identified) were polymorphic. This result showed a significantly higher success compared to our initial results of 51 (20.64%) polymorphic markers out of the 188 amplified when 247 previously reported markers were screened. The screening of two cultivars revealed that markers were efficient to identify up to three alleles. The characterization of these 69 new markers with 247 markers previously reported showed that di-nucleotide motifs were most abundant, followed by tri- and tetra-nucleotide motifs. TC motif markers were most polymorphic (12.08%) followed by AG and CT motifs (both 9.89%). Similarly, AGA (6.59%) and TATT (3.29%) were most polymorphic among the tri- and tetra-nucleotide motifs. These 69 hypervariable microsatellite markers along with 188 markers initially validated in this study shall be useful for phylogenetic analyses, studies of linkage, QTL, and association mapping in bitter melon.

Stomata are essential pores flanked by guard cells that control gas exchange in plants. We can utilize stomatal size and density measurements as a proxy for a plant's capacity for gas exchange. While stomatal responses to stressful environments are well studied; data are lacking in the responses across mutant genotypes of the same species in these trait and treatment interactions or genetic variation in phenotypic plasticity. We evaluated the effects of soil nutrient variation on macroscopic and stomatal traits of Arabidopsis thaliana T-DNA insertion mutants for which prior performance in a single benign growing condition were available. Nutrient-induced stress significantly impacted traits including plant biomass, height, fruit number, and leaf number which we denote as macroscopic traits. We found evidence that genotype by environment effects exist for macroscopic traits, yet total stomatal area variation, or "microscopic variation" across environments was modest. Divergence from the wildtype line varied by mutant background and these responses were variable among traits. These findings suggest that Arabidopsis employs a strategy of physiological compensation, sacrificing morphological traits to maintain stomatal production.

Identifying which species exhibit polyandry may lead to further insights into evolutionary biology and social behaviour. However, confirming polyandry can be difficult. High-resolution genetics provides a useful means to gain evidence. Although the threatened Pelodryadid frog, the green and golden bell frog Litoria aurea, has been subject to numerous ecological studies, there is uncertainty surrounding its reproductive ecology. Polyandry has not been formally identified in L. aurea or any species within the Pelodryadidae family. We aimed to identify if there was genetic evidence of polyandry in a population occurring in a wetland complex on Kooragang Island, New South Wales. To accomplish this, we collected genetic samples of tadpoles within the same size cohort about 20-30 days after explosive breeding events. Genotypes of 14 females, nine males and 70 tadpoles were analysed with COLONY (1988 single nucleotide polymorphisms after filtering) to identify parentage, full-siblings and half-siblings. We found support for the hypothesis that L. aurea is polyandrous. Based on previous observations of multi-male matings and the narrow time periods that breeding occurred in, it is likely this species exhibits simultaneous polyandry. We discuss these results in regards to behavioural adaptive processes and avenues for further research.

Reducing false discoveries caused by population stratification (PS) has always been a challenge in genome-wide association studies (GWAS). The current literature established several single marker approaches including genomic control (GC), EIGENSTRAT and generalized linear mixed model association test (GMMAT) and multi-marker methods such as LASSO mixed model (LASSOMM). However, the single-marker methods require prespecifying an arbitrary p value threshold in the selection process, likely resulting in suboptimal precision or recall. On the other hand, it appears that LASSOMM is extremely computationally intensive and may not suitable for large-scale GWAS. In this paper, we proposed a simple multi-marker approach (PCA-LASSO) combining principal component analysis (PCA) and least absolute shrinkage and selection operator (LASSO). We utilize PCA to correct for the confounding effects of PS and LASSO with built-in cross-validation for a data-driven selection. Compared to the current single-marker approaches, the proposed PCA-LASSO provides optimal balance between precision and recall, and consequently superior F₁ scores. Similarly, compared to LASSOMM, PCA-LASSO markedly increases the precision while minimizing the loss of recall, and therefore improves the overall F₁ score in presence of PS. More importantly, PCA-LASSO drastically reduces the computational time by > 1000 times when compared to LASSOMM. We applied PCA-LASSO to a real dataset of Alzheimer's disease and successfully identified SNP rs429358 (Gene APOE4) which has been widely reported to be associated with the onset and elevated risk of Alzheimer's disease. In conclusion, PCA-LASSO is a simple, fast, but accurate approach for GWAS in presence of latent PS.

The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.

Analysis of the mtDNA variation in Apis mellifera L. has allowed distinguishing subspecies and evolutionary lineages by means of different molecular methods; from RFLP, to PCR-RFLP and direct sequencing. Likewise, geometric morphometrics (GM) has been used to distinguish Africanized honey bees with a high degree of consistency with studies using molecular information. High-resolution fusion analysis (HRM) allows one to quickly identify sequence polymorphisms by comparing DNA melting curves in short amplicons generated by real-time PCR (qPCR). The objective of this work was to implement the HRM technique in the diagnosis of Africanization of colonies of A. mellifera from Argentina, using GM as a validation method. DNA was extracted from 60 A. mellifera colonies for mitotype identification. Samples were initially analyzed by HRM, through qPCRs of two regions (485 bp/385 bp) of the mitochondrial cytochrome b gene (cytb). This technique was then optimizing to amplify a smaller PCR product (207 bp) for the HRM diagnosis for the Africanization of colonies. Of the 60 colony samples analyzed, 41 were classified as colonies of European origin whereas 19 revealed African origin. All the samples classified by HRM were correctly validated by GM, demonstrating that this technique could be implemented for a rapid identification of African mitotypes in Apis mellifera samples.

Fire ants (Solenopsis invicta Buren in J Ga Entomol Soc 7:1-26, 1972), an invasive alien ant species, first spread from South America to the United States in the 1930s, the southern part of the United States by the end of the twentieth century, Oceania, Taiwan, and China in the twenty-first century, and finally to Japan and South Korea in 2017. As these ants have significant negative economic, human health, and environmental impacts, the purpose of this research was to accumulate cytogenetic information regarding fire ants and provide basic data for developing management strategies for their control. Fire ants were collected from invasive populations from Taiwan, Florida (USA), and Buenos Aires (Argentina), and a native population from Puerto Iguazu (Argentina), their point of origination, and analyzed with regard to chromosome number, morphology, and polyploidy, silver-stained nucleolar organizer regions (Ag-NORs), and 18S rDNA and telomere fluorescence in situ hybridization (FISH). The results showed that (1) fire ants from invaded populations differed in chromosome morphology compared to those from native populations; (2) the Florida and Taiwanese fire ant populations evinced greater variability in chromosome numbers and polyploidy variations; (3) the Taiwanese population exhibited significantly increased Ag-NOR signals in interphase cells, with signal number significantly positively correlating with distance from native populations; and (4) substantial diversity of signals was also apparent following 18S rDNA and telomere FISH analyses. Variation in these characteristics were hypothesized to be due to (1) the effect of hybridizations and interbreeding between closely related species or genetically distant populations, and (2) the potential effect of large amounts of insecticides sprayed for pest control.

Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.

The biological meaning of low complexity regions in the proteins of Plasmodium species is a topic of discussion in evolutionary biology. There is a debate between selectionists and neutralists, who either attribute or do not attribute an effect of low-complexity regions on the fitness of these parasites, respectively. In this work, we comparatively study 22 Plasmodium species to understand whether their low complexity regions undergo a neutral or, rather, a selective and species-dependent evolution. The focus is on the connection between the codon repertoire of the genetic coding sequences and the occurrence of low complexity regions in the corresponding proteins. The first part of the work concerns the correlation between the length of plasmodial proteins and their propensity at embedding low complexity regions. Relative synonymous codon usage, entropy, and other indicators reveal that the incidence of low complexity regions and their codon bias is species-specific and subject to selective evolutionary pressure. We also observed that protein length, a relaxed selective pressure, and a broad repertoire of codons in proteins, are strongly correlated with the occurrence of low complexity regions. Overall, it seems plausible that the codon bias of low-complexity regions contributes to functional innovation and codon bias enhancement of proteins on which Plasmodium species rest as successful evolutionary parasites.