Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to an Italian wolf mtDNA genome (TN93 and p-distances = 0.0012), five to seven times shorter than divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 -0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 4000 -21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin and population dynamics before the extinction of wolves in Sicily.
Spilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock’s eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages—”zero sign of disease” and “evident sign of infection”. Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. ‘Koroneiki’ showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in ‘Koroneiki’, while ‘Nocellara del Belice’ was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.
20Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA 21 genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of 22 Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of 23 historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to 24 an Italian wolf mtDNA genome (TN93 and p-distances = 0.0012), five to seven times shorter than 25 divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 -26 0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 27 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of 28 divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 29 4000 -21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from 30 southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of 31 Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin 32 and population dynamics before the extinction of wolves in Sicily. 33 34
Four chimpanzee subspecies (Mammalia Hominidae) are commonly recognised: the Western Chimpanzee, P. troglodytes verus (Schwarz, 1934), the Nigeria-Cameroon Chimpanzee, P. troglodytes ellioti, the Central Chimpanzee, P. troglodytes troglodytes (Blumenbach, 1799), and the Eastern Chimpanzee, P. troglodytes schweinfurthii (Giglioli, 1872). Recent studies on mitochondrial DNA show the incorporation of P. troglodytes schweinfurthii in P. troglodytes troglodytes, suggesting the existence of only two subspecies: P. troglodytes troglodytes in Central and Eastern Africa and P. troglodytes verus-P. troglodytes ellioti in West Africa. The aim of the present study is twofold: first, to identify the correct subspecies of two chimpanzee samples collected in a Biopark structure in Carini (Sicily, Italy), and second, to verify whether there was a kinship relationship between the two samples through techniques such as DNA barcoding and microsatellite analysis. DNA was extracted from apes' buccal swabs, the cytochrome oxidase subunit 1 (COI) gene was amplified using universal primers, then purified and injected into capillary electrophoresis Genetic Analyzer ABI 3130 for sequencing. The sequence was searched on the NCBI Blast database. In addiction, the microsatellite analysis was performed on the same machine for parentage detection among samples, and data were analyzed with GenMapper software. Our results show that both samples were P. troglodytes troglodytes, while the analysis of the microsatellite results in an unclear relationship between two chimpanzee samples.
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