Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume <it>Phaseolus vulgaris </it>(common bean). Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS) technology to identify and characterize the miRNA population of <it>Phaseolus vulgaris</it>.</p> <p>Results</p> <p>Small RNA libraries were generated from roots, flowers, leaves, and seedlings of <it>P. vulgaris</it>. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies.</p> <p>Conclusions</p> <p>This work represents the first massive-scale RNA sequencing study performed in <it>Phaseolus vulgaris </it>to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of <it>P. vulgaris </it>miRNAs in relation to those of other legumes.</p

The confining-Higgs phase transition in U(1)-Higgs LGT

Abstract We simulate the compact U(1)-Higgs model in a four-dimensional lattice. We present a numerical study for the behaviour around the region where the transition between the confining and Higgs phases disappears. The transition line is found to be first order and to end in a second-order point. We measure the critical exponents of the endpoint obtaining the mean field ones within errors

Prevalence and genetic characteristics of Staphylococcus aureus CC398 isolates from invasive infections in spanish hospitals, focusing on the livestock-independent CC398-MSSA clade

Background: Livestock-associated (LA)-CC398-MRSA is closely related to pigs, being unfrequently detected in human invasive infections. CC398-MSSA is emerging in human invasive infections in some countries, but genetic and epidemiological characteristics are still scarcely reported. Objectives: To determine the prevalence of Staphylococcus aureus (SA) CC398, both MRSA and MSSA, among blood cultures SA isolates recovered in Spanish hospitals located in regions with different pig-farming densities (PD) and characterize the recovered isolates. Methods: One thousand twenty-two SA isolates (761 MSSA, 261 MRSA) recovered from blood cultures during 6–12 months in 17 Spanish hospitals (2018–2019) were studied. CC398 lineage identification, detection of spa-types, and antibiotic resistance, virulence and human immune evasion cluster (IEC) genes were analyzed by PCR/sequencing. Results: Forty-four CC398-MSSA isolates (4.3% of SA; 5.8% of MSSA) and 10 CC398-MRSA isolates (1% of SA; 3.8% of MRSA) were detected. Eleven spa-types were found among the CC398-MSSA isolates with t571 and t1451 the most frequent spa-types detected (75%). Most of CC398-MSSA isolates were Immune-Evasion-Cluster (IEC)-positive (88.6%), tetracycline-susceptible (95.5%) and erythromycin/clindamycin–inducible-resistant/erm(T)-positive (75%). No statistical significance was detected when the CC398-MSSA/MSSA rate was correlated to PD (pigs/km2) (p = 0.108). On the contrary, CC398-MRSA isolates were all IEC-negative, predominately spa-t011 (70%), and the CC398-MRSA/MRSA rate was significantly associated to PD (p < 0.005). Conclusion: CC398-MSSA is an emerging clade in invasive infections in Spanish hospitals. CC398-MRSA (mostly t011) and CC398-MSSA (mostly t571 and t1451) show important differences, possibly suggesting divergent steps in host-adaptation evolutionary processes. While CC398-MRSA is livestock-associated (lacking IEC-system), CC398-MSSA seems to be mostly livestock-independent, carrying human-adaptation markers.

Bycatch of franciscana dolphins Pontoporia blainvillei and the dynamic of artisanal fisheries in the species' southernmost area of distribution

Na Argentina, a toninha é um dos cetáceos mais vulneráveis devido às capturas por rede de pesca artesanal. O presente estudo teve como objetivo estimar as capturas acidentais no sul da província de Buenos Aires, através de entrevistas aos capitães de barcos de pesca artesanal, entre os anos 2006-2009. As capturas foram reportadas para redes de emalhe e de camarão; com as mais altas frequências entre outubro e fevereiro, a 5 km da costa e 10-20 m de profundidade. A mortalidade acidental média anual estimada foi de 107 golfinhos (IC 95% = 87-129), 92 em redes de emalhe (IC 95% = 73-112) e 15 em redes de camarão (IC 95% = 8-25), com uma captura de 0,029 golfinhos/km de rede de emalhe (IC 95% = 0,023-0,036) e 0,024/rede de camarão (IC 95% = 0,012-0,035). As flutuações anuais responderam principalmente às diferenças nos dias de pesca. Considerando o último levantamento estimativo feito para o norte costeiro da província, estima-se uma mortalidade entre 360-539 golfinhos/ano em toda a província de Buenos Aires. Esses valores correspondem de 2,5-3,7% da abundância populacional da Argentina; o que traria como consequência um declínio populacional da espécie, tornando-se fundamental encontrar alternativas de pesca para a área.In Argentina, the franciscana dolphin is one of the most vulnerable cetaceans regularly entangled in coastal artisanal fishery nets. The aim of this paper is to estimate the species' incidental mortality on the Southern coast of Buenos Aires province through interviews with the captains of artisanal fishing vessels, in the period 2006-2009. Franciscana bycatch was reported for gillnets and shrimper gear all year round but it occurred more frequently between October and February, at 5 km offshore and 10-20 m depth. The estimated mean annual incidental mortality was 107 dolphins (CI 95% = 87-129), 92 caught in gillnets (CI 95% = 73-112) and 15 in shrimpers' gear (CI 95% = 8-25) with a capture per unit effort of 0.029 dolphins per km of gillnet (CI 95% = 0.023-0.036) and 0.022 per shrimpe r's net (CI 95% = 0.012-0.035). Annual fluctuations were due to differences in the number of gillnetting fishing days. If mortality estimates for the Northern coast are also taken into account, values attain a maximum of 360-539 dolphins bycaught in the entire Buenos Aires province, representing 2.5-3.7% of the species' abundance in Argentina. This will inevitably lead to the decline of franciscana dolphin populations in the near future unless alternative fishing grounds are identified and alternative gearadopted

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.Conclusions: We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.Peer reviewedBiochemistry and Molecular Biolog

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads

Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with AISO patterns across various animal and plant species. Finally, we used Insplico to investigate AISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical AISO, in which the downstream intron is spliced first, and we suggest two potential modes of SRRM4 regulation of microexons related to their AISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [ERCCoG-LS2-101002275 to M.I.]; Spanish Ministry of Economy and Competitiveness [PID2020-115040GB-I00 to M.I.]; ‘Centro de Excelencia Severo Ochoa 2013–2017’ [SEV-2012-0208]. Funding for open access charge: European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [ERCCoG-LS2-101002275 to M.I.]