Examinando por Materia "Phylogenetics"

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Complete mitogenome of “pumpo” (Bos taurus), a top bull from a Peruvian genetic nucleus, and its phylogenetic analysis
(MDPI, 2024-05-28) Estrada Cañari, Richard; Figueroa Venegas, Deyanira Antonella; Romero Avila, Yolanda; Alvarez García, Wuesley Yusmein; Rojas Cruz, Diorman; Alvarado, Wigoberto; Maicelo, Jorge L.; Quilcate Pairazamán, Carlos Enrique; Arbizu Berrocal, Carlos Irvin
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.
Morphological, phylogenetic, and genomic evidence reveals the causal agent of thread blight disease of cacao in Peru is a new species of Marasmius in the section Neosessiles, Marasmius infestans sp. nov.
(F1000Research, 2024-01-29) Huamán Pilco, Ángel Fernando; Ramos Carrasco, Tito Ademir; Ernesto Franco, Mario Emilio; Tineo Flores, Daniel; Estrada Cañari, Richard; Romero, Pedro Eduardo; Aguilar Rafael, Vilma; Ramírez Orrego, Lourdes Adriana; Tincopa Marca, Rosalina; Márquez, Fanny Rosario; Oliva Cruz, Manuel; Díaz Valderrama, Jorge Ronny
The thread blight disease (TBD) of cacao (Theobroma cacao) in the department of Amazonas, Peru was recently reported to be caused by Marasmius tenuissimus (Sect. Neosessiles). This same species is known to be the main causal agent of TBD in West Africa. However, some morphological characteristics, such as the presence of rhizomorphs, the almost exclusively white color, and pileus sizes less than 5 mm, among others, differ to the description of M. tenuissimus. Therefore, we aimed to conduct a taxonomic revision of the cacao-TBD causal agent in Peru, by using thorough micro and macro morphological, phylogenetic, and nuclear and mitochondrial genomic approaches. We showed that the causal agent of TBD of cacao in Amazonas, Peru, belongs to a new species, Marasmius infestans sp. nov. This study enriches our knowledge of species in the Sect. Neosessiles, and strongly suggests that the M. tenuissimus species complex is highly diverse.
Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies
(Sociedade Brasileira de Genética, 2022-01-21) Balbinott, Natalia; Ferreira Rodrigues, Nureyev; Guzman Escuredo, Frank Lino; Turchetto Zolet, Andreia Carina; Margis, Rogerio
Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny.
The phylogeography of potato virus X shows the fingerprints of its human vector
(MDPI, 2021-09-09) Fuentes, Segundo; Gibbs, Adrian J.; Hajizadeh, Mohammad; Perez, Ana; Adams, Ian P.; Fribourg, Cesar E.; Kreuze, Jan; Fox, Adrian; Boonham, Neil; Jones, Roger A. C.
Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop′s main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato’s domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A–D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX′s entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.