Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing ( q-value < 0.05 and ☐.6 log 2fold-change), being upregulated in HIGH pigs. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs ( P-value < 0.01 and ☐.6 log 2fold-change). Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. There are no files associated with this item.The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. Plum bark necrosis stem pitting-associated virus Instituto Nacional de Investigaciones Agrarias (INIA) E-RTA2017-00009 grant 10’7, 46113 Moncada (Valencia), EspañaĬentro de Protección Vegetal y Biotecnología Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, Km. The American Phytopathological Society (APS) Journalsįirst report of Plum bark necrosis stem pitting-associated virus in sweet cherry in Spain To our knowledge this is the first report of PBNSPaV infecting sweet cherry in Spain, contributing to a better understanding of the epidemiology and host range distribution of this pathogen. It is interesting to note that stem pitting and bark symptoms were not observed in any of the samples analysed. Seven of these samples were positive for PBNSPaV, further confirming the presence of the virus in sweet cherry in Spain. A total of 24 samples collected from the same cherry growing area were tested by RT-PCR using the same primers. The 301 bp PCR product obtained (MN240523) was sequenced by Sanger and confirmed with 100% of identity the P7 sequence recovered by HTS (excluding the primers used for amplification). In order to confirm the presence of PBNSPaV in sample P7, amplification of a partial region of the CP gene by RT-PCR was carried out using the specific primers PBN-CP-F and PBN-CP-R (Zamorano et al. The nucleotide identity between P7 isolate and Pair-2 was 99,27%.
The best mapping results were obtained using the isolate Pair-2 (KC590345) from France as reference, allowing the recovery of a 14,199 nt sequence, representing P7 isolate's almost full length genome (GenBank accession number MN228561). Further analysis by mapping the reads against all the full length PBNSPaV sequences available in the databases was performed using Geneious software. Cherry virus A (CVA) was also detected in this step, with part of its genomic sequence represented in 11 contigs. This analysis showed that 8 contigs were related to PBNSPaV, indicating the presence of this virus in sample P7. A total of 6,270 contigs (average size 1,884 nt) were de novo assembled by CLC and subsequently analysed by BlastN and BlastX. After a quality control step conducted by CLC, sample P7, yielded 42,683,262 pair-end HTS reads (150 nt each). Data analysis was performed using CLC Genomics Workbench 10.1.1 and Geneious 9.1.8 softwares. Total RNA purified from leaves was sequenced using RNAseq TrueSeq Illumina technology including viral enrichment step by ribo-depletion. Planera, showing reddening and necrotic spots on the leaves was analysed by High throughput sequencing (HTS) on a Nextseq 500 platform. In the frame of this survey, one sample (P7) from a sweet cherry tree (Prunus avium), c.v. In summer 2017, a survey was conducted in a small cherry growing area in the eastern region of Spain (Planes, Alicante). PBNSPaV has been described to infect apricot in Spain (García-Ibarra et al. Since then PBNSPaV has been shown to be worldwide distributed, affecting a broad range of Prunus species (Matic et al. PBNSPaV was reported for the first time infecting plum trees (Prunus salicina Lindl.) in Dinuba, CA, U.S.A. Plum bark necrosis stem pitting-associated virus (PBNSPaV) is a viral species that belongs to the genus Ampelovirus, family Closteroviridae. First report of Plum bark necrosis stem pitting-associated virus in sweet cherry in Spain.