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Ítem The complete chloroplast genome of the national tree of Peru, quina (Cinchona officinalis L., Rubiaceae)(Taylor & Francis, 2021-09-06) Arbizu Berrocal, Carlos Irvin; Ferro Mauricio, Rubén Darío; Chávez Galarza, Julio César; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge LuisHere, we report the first complete chloroplast (cp) genome of Cinchona officinalis. This cp genome has a 156,984 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (83,929 bp) and an 18,051 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (27,502 bp). The total GC content was 37.75%. Quina tree chloroplast genome possesses 135 genes that consisted of 89 protein-coding genes, 37 tRNA, eight rRNA, and one pseudogene. Phylogenetic analysis showed that C. officinalis is sister to C. pubescens and sister to them is Isertia laevis; all belong to the Cinchonoideae sub-family.Ítem Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)(Springer Nature, 2016-10-28) Arbizu Berrocal, Carlos Irvin; Ellison, Shelby L.; Senalik, Douglas; Simon, Philipp W.; Spooner, David M.Results: We used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic. Conclusions: Our study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in DaucusÍtem 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 IrvinThe 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.Ítem Implementing cloud computing for the digital mapping of agricultural soil properties from high resolution UAV multispectral imagery(MDPI, 2023-06-20) Pizarro Carcausto, Samuel Edwin; Pricope, Narcisa G.; Figueroa Venegas, Deyanira Antonella; Carbajal Llosa, Carlos Miguel; Quispe Huincho, Miriam Rocío; Vera Vilchez, Jesús Emilio; Alejandro Méndez, Lidiana Rene; Achallma Mendoza, Lino; González Tovar, Izamar Estrella; Salazar Coronel, Wilian; Loayza, Hildo; Cruz Luis, Juancarlos Alejandro; Arbizu Berrocal, Carlos IrvinThe spatial heterogeneity of soil properties has a significant impact on crop growth, making it difficult to adopt site-specific crop management practices. Traditional laboratory-based analyses are costly, and data extrapolation for mapping soil properties using high-resolution imagery becomes a computationally expensive procedure, taking days or weeks to obtain accurate results using a desktop workstation. To overcome these challenges, cloud-based solutions such as Google Earth Engine (GEE) have been used to analyze complex data with machine learning algorithms. In this study, we explored the feasibility of designing and implementing a digital soil mapping approach in the GEE platform using high-resolution reflectance imagery derived from a thermal infrared and multispectral camera Altum (MicaSense, Seattle, WA, USA). We compared a suite of multispectral-derived soil and vegetation indices with in situ measurements of physical-chemical soil properties in agricultural lands in the Peruvian Mantaro Valley. The prediction ability of several machine learning algorithms (CART, XGBoost, and Random Forest) was evaluated using R2, to select the best predicted maps (R2 > 0.80), for ten soil properties, including Lime, Clay, Sand, N, P, K, OM, Al, EC, and pH, using multispectral imagery and derived products such as spectral indices and a digital surface model (DSM). Our results indicate that the predictions based on spectral indices, most notably, SRI, GNDWI, NDWI, and ExG, in combination with CART and RF algorithms are superior to those based on individual spectral bands. Additionally, the DSM improves the model prediction accuracy, especially for K and Al. We demonstrate that high-resolution multispectral imagery processed in the GEE platform has the potential to develop soil properties prediction models essential in establishing adaptive soil monitoring programs for agricultural regions.Ítem Extended studies of interspecific relationships in Daucus (Apiaceae) using DNA sequences from ten nuclear orthologues(Oxford University, 2019-09-24) Martínez Flores, Fernando; Crespo, Manuel B.; Geoffriau, Emmanuel; Allender, Charlotte; Ruess, Holly; Arbizu Berrocal, Carlos Irvin; Simon, Philipp W.; Spooner, David M.Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated.Ítem Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species(MDPI, 2022-09-01) Saldaña Serrano, Carla Lizet; Chávez Galarza, Julio César; De la Cruz, Germán; Jhoncon, Jorge H.; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Arbizu Berrocal, Carlos IrvinSweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources.Ítem Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers(MDPI, 2021-08-22) Saldaña Serrano, Carla Lizet; Cancan, Johan D.; Cruz Hilacondo, Wilbert Eddy; Correa, Mirian; Ramos León, Haydeé Miriam; Cuellar Bautista, José Eloy; Arbizu Berrocal, Carlos IrvinCapirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.Ítem Changes in bulk and rhizosphere soil microbial diversity communities of native quinoa due to the monocropping in the Peruvian Central Andes(MDPI, 2023-07-28) Estrada Cañari, Richard; Cosme de la Cruz, Roberto Carlos; Porras Valencia, Angie Tatiana; Reynoso Zárate, Auristela Florencia; Calderon, Constatino; Arbizu Berrocal, Carlos Irvin; Arone, Gregorio J.Quinoa (Chenopodium quinoa) is a highly nutritious crop that is resistant to adverse conditions. Due to the considerable increase in its commercial production in Andean soils, the plant is suffering the negative effects of monocropping, which reduces its yield. We used for the first time a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the bulk and rhizosphere in soils of native C. quinoa affected by monocropping in the central Andes of Peru. The results showed that the bacterial and fungal community structure among the treatments was significantly changed by the monocropping and the types of soil (rhizosphere and bulk). Also, in soils subjected to monocropping, there was an increase in Actinobacteria and a decrease in Proteobacteria, and the reduction in the presence of Ascomycota and the increase in Basidiomycota. By alpha-diversity indices, lower values of bacteria and fungi were observed in the monoculture option compared to the soil not affected by monocropping, and sometimes significant differences were found between both. We detected differentially abundant phytopathogenic fungi and bacteria with growth-stimulating effects on plants. Also, we denoted a decrease in the abundance of the functional predictions in bacteria in the monocropped soils. This research will serve as a starting point to explore the importance and effects of microorganisms in degraded soils and their impact on the growth and quality of quinoa crops.Ítem Unlocking the complete chloroplast genome of a native tree species from the Amazon Basin, capirona (Calycophyllum spruceanum, Rubiaceae), and Its comparative analysis with other Ixoroideae species(MDPI, 2022-01-07) Saldaña Serrano, Carla Lizet; Rodriguez Grados, Pedro Manuel; Chávez Galarza, Julio César; Feijoo Narvasta, Shefferson Gilbert Wilson; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Jhoncon, Jorge H.; Arbizu Berrocal, Carlos IrvinCapirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.Ítem Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru(Elsevier, 2024-04-24) Corredor Arizapana, Flor Anita; Figueroa Venegas, Deyanira Antonella; Estrada Cañari, Richard; Burgos Paz, William; Salazar Coronel, Wilian; Cruz Góngora, Wilder; Lobato Gálvez, Roiser Honorio; Injante Silva, Pedro Hugo; Godoy Padilla, David José; Barrantes Bravo, Christian Alfredo; Ganoza Roncal, Jorge Juan; Cruz Luis, Juancarlos Alejandro; Arbizu Berrocal, Carlos IrvinGoat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production geographical departments in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p < 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.