bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement of rice blast resistance by developing monogenic lines, two-gene pyramids and three-gene pyramid through MAS
Authors: Xiao Wuming , Yang Qiyun , Huang Ming , Guo Tao , Liu Yongzhu , Wang Jiafeng , Yang Guili , Zhou Jiyong , Yang Jianyuan , Zhu Xiaoyuan , Chen Zhiqiang , Wang Hui 
Published: November 2019

AbstractBackgroundRice blast caused byMagnaporthe oryzae(M. oryzae) is one of the most destructive diseases in rice production. Development of resistant varieties through pyramiding of resistant (R) genes is considered as an effective strategy to cope with the disease. However, is it really essential to pyramid moreRgenes in a specific ecological regions? To answer this question, a set of rice improved lines were developed in this study. Afterwards, the blast disease resistance and agronomic traits of the recurrent parent (RP), donor parents (DPs) and improved lines were investigated.ResultsWe developed seven improved lines, comprising three monogenic lines, three two-gene pyramids and one three-gene pyramid, by introgression ofRgene(s) into a common genetic background using marker-assisted backcross breeding (MABB). Based on 302 SSR markers, the recurrent genome of the seven improved lines reached a range of 89.1 to 95.5%, with the average genome recovery of 92.9%. The pathogenicity assays inoculated with 32 different blast isolates under artificial conditions showed that the resistance spectrum of all the improved lines was significantly broadened. The assays further showed that the two-gene pyramids and the three-gene pyramid exhibited wider resistance spectrum than the monogenic lines. At natural nurseries, the three monogenic lines still showed high ratios of infected panicles, whereas the two-gene pyramids and the three-gene pyramid showed high level of panicle blast resistance. However, the two-gene pyramid R504 reached the similar resistance effect of the three-gene pyramid R507 considering resistance spectrum under artificial conditions and panicle blast resistance under field conditions. Generally, the improved lines showed comparable agronomic traits compared with the recurrent parent (RP), but the three-gene pyramid showed reduced grain yield per plant.ConclusionsAll the improved lines conferred wider resistance spectrum compared with the RP. Yet, the three monogenic lines did not work under field conditions of the two nurseries. Given the similar performances on the main agronomic traits as the RP, the two-gene pyramids have achieved the breeding goals of broad resistance spectrum and effective panicle blast resistance. Whereas, the three-gene pyramid harboringPi2,Pi46andPitaseems superfluous considering its reduced yield, although it also showed displayed high level of blast resistance. Thus, rational use ofRgenes rather than stacking moreRgenes is recommended to control the disease.
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis
Authors: Licursi Valerio , Conte Federica , Fiscon Giulia , Paci Paola 
Published: November 2019

Abstract

Background
miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis.

Results
We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components.

Conclusion
MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses by using only a single tool leading to a more effective prioritization of the miRNA-target interactions. This has the potential to avoid researchers without computational and informatics skills to navigate multiple websites and thus to independently investigate miRNA activity in every cellular process of interest in an easy and at the same time exhaustive way thanks to the intuitive web interface. The web application along with a well-documented and comprehensive user guide are freely available at http://userver.bio.uniroma1.it/apps/mienturnet/
without any login requirement.
Evidence for adaptive introgression of exons across a hybrid swarm in deer
Authors: Haines Margaret L. , Luikart Gordon , Amish Stephen J. , Smith Seth , Latch Emily K. 
Published: November 2019

AbstractBackgroundSecondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes.ResultsWe observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat.ConclusionsOur data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.
Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages
Authors: Yan Mengxiao , Liu Ruibin , Li Ying , Hipp Andrew L. , Deng Min , Xiong Yanshi 
Published: November 2019

AbstractBackgroundUnderstanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genusQuercusis a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere.Quercusthus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore,Quercusprovides a deep insight into how tree species will respond to future climate change. This study investigated whether closely relatedQuercuslineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures.ResultsDespite their close relationships, the three main oak lineages (QuercussectionsCyclobalanopsis,Ilex, andQuercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in sectionCyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in sectionIlex, which is due to their long-term isolation and strong local adaptation.The widespread sectionQuercusis distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America.ConclusionsGenetic variations of sectionsIlexandQuercuswere significantly predicted by geographic and climate variations, while those of sectionCyclobalanopsiswere poorly predictable by geographic or climatic diversity.Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.
Nest defense in the face of cuckoldry: evolutionary rather than facultative adaptation to chronic paternity loss
Authors: Zimmermann Holger , Fritzsche Karoline , Henshaw Jonathan M. , Katongo Cyprian , Banda Taylor , Makasa Lawrence , Sefc Kristina M. , Bose Aneesh P. H. 
Published: November 2019

AbstractBackgroundRaising unrelated offspring is typically wasteful of parental resources and so individuals are expected to reduce or maintain low levels of parental effort when their parentage is low. This can involve facultative, flexible adjustments of parental care to cues of lost parentage in the current brood, stabilizing selection for a low level of paternal investment, or an evolutionary reduction in parental investment in response to chronically low parentage.ResultsWe studied parental care inVariabilichromis moorii, a socially monogamous, biparental cichlid fish, whose mating system is characterized by frequent cuckoldry and whose primary form of parental care is offspring defense. We combine field observations with genetic parentage analyses to show that while both parents defend their nest against intruding con- and hetero-specifics, males and females may do so for different reasons. Males in the study group (30 breeding pairs) sired 0–100% (median 83%) of the fry in their nests. Males defended less against immediate threats to the offspring, and more against threats to their territories, which are essential for the males’ future reproductive success. Males also showed no clear relationship between their share of defense and their paternity of the brood. Females, on the other hand, were related to nearly all the offspring under their care, and defended almost equally against all types of threats.ConclusionOverall, males contributed less to defense than females and we suggest that this asymmetry is the result of an evolutionary response by males to chronically high paternity loss in this species. Although most males in the current study group achieved high parentage in their nests, the average paternity inV. moorii, sampled across multiple seasons, is only about 55%. We highlight the importance and complexity of studying nest defense as a form of parental care in systems where defense may serve not only to protect current offspring, but also to ensure future reproductive success by maintaining a territory.
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
Authors: Burkhardt Alyssa K. , Childs Kevin L. , Wang Jie , Ramon Marina L. , Martin Frank N. 
Published: November 2019

AbstractBackgroundMacrophomina phaseolinais a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.ResultsWe used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies forM. phaseolinaisolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.ConclusionsHigh-quality reference genomes ofM. phaseolinahave allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.
Clarification of the dispensability of PDX1.2 for Arabidopsis viability using CRISPR/Cas9
Authors: Dell’Aglio Elisa , Dalvit Ivan , Loubéry Sylvain , Fitzpatrick Teresa B. 
Published: November 2019

Abstract

Background
PDX1.2 has recently been shown to be a regulator of vitamin B6 biosynthesis in plants and is implicated in biotic and abiotic stress resistance. PDX1.2 expression is strongly and rapidly induced by heat stress. Interestingly, PDX1.2 is restricted to eudicota, wherein it behaves as a non-catalytic pseudoenzyme and is suggested to provide an adaptive advantage to this clade. A first report on an Arabidopsis insertion mutant claims that PDX1.2 is indispensable for viability, being essential for embryogenesis. However, a later study using an independent insertion allele suggests that knockout mutants of pdx1.2 are viable. Therefore, the essentiality of PDX1.2 for Arabidopsis viability is a matter of debate. Given the important implications of PDX1.2 in stress responses, it is imperative to clarify if it is essential for plant viability.

Results
We have studied the previously reported insertion alleles of PDX1.2, one of which is claimed to be essential for embryogenesis (pdx1.2–1), whereas the other is viable (pdx1.2–2). Our study shows that pdx1.2–1 carries multiple T-DNA insertions, but the T-DNA insertion in PDX1.2 is not responsible for the loss of embryogenesis. By contrast, the pdx1.2–2 allele is an overexpressor of PDX1.2 under standard growth conditions and not a null allele as previously reported. Nonetheless, upregulation of PDX1.2 expression under heat stress is impaired in this mutant line. In wild type Arabidopsis, studies of PDX1.2-YFP fusion proteins show that the protein is enhanced under heat stress conditions. To clarify if PDX1.2 is essential for Arabidopsis viability, we generated several independent mutant lines using the CRISPR-Cas9 gene editing technology. All of these lines are viable and behave similar to wild type under standard growth conditions. Reciprocal crosses of a subset of the CRISPR lines with pdx1.2–1 recovers viability of the latter line and demonstrates that knocking out the functionality of PDX1.2 does not impair embryogenesis.

Conclusions
Gene editing reveals that PDX1.2 is dispensable for Arabidopsis viability and resolves conflicting reports in the literature on its function.
A mutant allele of ζ-carotene isomerase (Z-ISO) is associated with the yellow pigmentation of the “Pinalate” sweet orange mutant and reveals new insights into its role in fruit carotenogenesis
Authors: Rodrigo María J. , Lado Joanna , Alós Enriqueta , Alquézar Berta , Dery Orly , Hirschberg Joseph , Zacarías Lorenzo 
Published: November 2019

Abstract

Background
Fruit coloration is one of the main quality parameters of Citrus fruit primarily determined by genetic factors. The fruit of ordinary sweet orange (Citrus sinensis) displays a pleasant orange tint due to accumulation of carotenoids, representing β,β-xanthophylls more than 80% of the total content. ‘Pinalate’ is a spontaneous bud mutant, or somatic mutation, derived from sweet orange ‘Navelate’, characterized by yellow fruits due to elevated proportions of upstream carotenes and reduced β,β-xanthophylls, which suggests a biosynthetic blockage at early steps of the carotenoid pathway.

Results
To identify the molecular basis of ‘Pinalate’ yellow fruit, a complete characterization of carotenoids profile together with transcriptional changes in carotenoid biosynthetic genes were performed in mutant and parental fruits during development and ripening. ‘Pinalate’ fruit showed a distinctive carotenoid profile at all ripening stages, accumulating phytoene, phytofluene and unusual proportions of 9,15,9′-tri-cis- and 9,9′-di-cis-ζ-carotene, while content of downstream carotenoids was significantly decreased. Transcript levels for most of the carotenoid biosynthetic genes showed no alterations in ‘Pinalate’; however, the steady-state level mRNA of ζ-carotene isomerase (Z-ISO), which catalyses the conversion of 9,15,9′-tri-cis- to 9,9′-di-cis-ζ-carotene, was significantly reduced both in ‘Pinalate’ fruit and leaf tissues. Isolation of the ‘Pinalate’ Z-ISO genomic sequence identified a new allele with a single nucleotide insertion at the second exon, which generates an alternative splicing site that alters Z-ISO transcripts encoding non-functional enzyme. Moreover, functional assays of citrus Z-ISO in E.coli showed that light is able to enhance a non-enzymatic isomerization of tri-cis to di-cis-ζ-carotene, which is in agreement with the partial rescue of mutant phenotype when ‘Pinalate’ fruits are highly exposed to light during ripening.

Conclusion
A single nucleotide insertion has been identified in ‘Pinalate’ Z-ISO gene that results in truncated proteins. This causes a bottleneck in the carotenoid pathway with an unbalanced content of carotenes upstream to β,β-xanthophylls in fruit tissues. In chloroplastic tissues, the effects of Z-ISO alteration are mainly manifested as a reduction in total carotenoid content. Taken together, our results indicate that the spontaneous single nucleotide insertion in Z-ISO is the molecular basis of the yellow pigmentation in ‘Pinalate’ sweet orange and points this isomerase as an essential activity for carotenogenesis in citrus fruits.
The effects of anesthesia induction and positive pressure ventilation on right-ventricular function: an echocardiography-based prospective observational study
Authors: Magunia Harry , Jordanow Anne , Keller Marius , Rosenberger Peter , Nowak-Machen Martina 
Published: November 2019

AbstractBackgroundGeneral anesthesia induction with the initiation of positive pressure ventilation creates a vulnerable phase for patients. The impact of positive intrathoracic pressure on cardiac performance has been studied but remains controversial. 3D echocardiography is a valid and MRI-validated bed-side tool to evaluate the right ventricle (RV). The aim of this study was to assess the impact of anesthesia induction (using midazolam, sufentanil and rocuronium, followed by sevoflurane) with positive pressure ventilation (PEEP 5, tidal volume 6–8 ml/kg) on 2D and 3D echocardiography derived parameters of RV function.MethodsA prospective observational study on fifty-three patients undergoing elective cardiac surgery in a tertiary care university hospital was designed. Transthoracic echocardiography exams were performed before and immediately after anesthesia induction and were recorded together with hemodynamic parameters and ventilator settings.ResultsAfter anesthesia induction TAPSE (mean difference − 1.6 mm (95% CI − 2.6 mm to − 0.7 mm;p = 0.0013) as well as the Tissue Doppler derived tricuspid annulus peak velocity (TDITVs’) were significantly reduced (mean difference − 1.9% (95% CI: − 2.6 to − 1.2;p < 0.0001), but global right ventricular ejection fraction (RVEF;p = 0.1607) and right ventricular stroke volume (RVSV;p = 0.1838) did not change.ConclusionsThis data shows a preserved right ventricular ejection fraction and right ventricular stroke volume after anesthesia induction and initiation of positive pressure ventilation. However, the baso-apical right ventricular function is significantly reduced. Larger studies are needed in order to determine the clinical impact of these findings especially in patients presenting with impaired right ventricular function before anesthesia induction.Trial registrationRetrospecitvely registered, 6th June 2016, ClinicalTrials.gov IdentifierNCT02820727.