Search Results - "genome sequencing"

Target capture sequencing for the first Nigerian genotype I ASFV genome by Adeola, A.C., Luka, P.D., Xiang-Xiang Jiang, Zheng-Fei Cai, Oluwole, O.O., Xian Shi, Oladele, B.M., Olorungbounmi, T.O., Boladuro, B., Omotosho, O., Okoro, V.M.O., Dawuda, P.M., Olaogun, S.C., Sanke, O.J., Hai-Bing Xie, Bishop, Richard P., Jianlin Han, Jianbo Li, Ya-Ping Zhang, Min-Sheng Peng

“…The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1. This provides insight into the origin and relationship of ASFV strains from Nigeria and Italy. …”
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Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses by Bejerman, Nicolas Esteban, Dietzgen, Ralf Georg, Debat, Humberto Julio

“…The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. …”
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Signs of a phyllospheric lifestyle in the genome of the stress-tolerant strain Azospirillum brasilense Az19 by Garcia, Julia Elena, Labarthe, María Mercedes, Pagnussat, Luciana Anabella, Amenta, Melina Beatriz, Creus, Cecilia Mónica, Maroniche, Guillermo Andrés

“…The objective of this study was to determine and analyze the genomic sequence of strain Az19 as a means of identifying putative stress-adaptation mechanisms. …”
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Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple commongarden experiments of lodgepole pine by Liu, Yang, Erbilgin, Nadir, Cappa, Eduardo Pablo, Chen, Charles, Ratcliffe, Blaise, Wei, Xiaojing, Klutsch, Jennifer G., Ullah, Aziz, Sebastian Azcona, Jaime, Thomas, Barb R., El-Kassaby, Yousry A.

“…By establishing four common-garden test sites for five lodgepole pine populations in western Canada, combined with genomic sequencing, we revealed the decoupling pattern and genetic underpinnings of tradeoffs between height growth, drought resistance based on δ13C and dendrochronology, and metrics of pest resistance based on pest suitability ratings. …”
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Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina by Ibanez, Julia Magali, Zambrana Montaño, Romina Micaela, Gonzalez Carreras, Pamela Stefanía, Obregon, Veronica Gabriela, Irazoqui, Jose Matias, Vera, Pablo Alfredo, Lattar, Tatiana Elisabet, Blanco Fernandez, María D., Puebla, Andrea Fabiana, Amadio, Ariel, Torres, Carolina, Lopez Lambertini, Paola Maria

“…Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. …”
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Transcriptomic Survey of the Midgut of Anthonomus grandis (Coleoptera: Curculionidae) by Salvador, Ricardo, Perez Principi, Ricardo Dario, Berretta, Marcelo Facundo, Fernandez, Paula Del Carmen, Paniego, Norma Beatriz, Sciocco, Alicia Ines, Hopp, Horacio Esteban

“…In spite of its importance, little is known about its genome sequence and, more important, its specific expression in key organs like the midgut. …”
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Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data by Bejerman, Nicolas Esteban, Dietzgen, Ralf Georg, Debat, Humberto Julio

“…The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. …”
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Loquat (Eriobotrya japonica) is a New Natural Host of Apple Stem Pitting Virus by Morán, Félix, Canales, Celia, Olmos, Antonio, Ruiz-García, Ana B.

“…A close phylogenetic relationship between ASPV-SL61 and ASPV-YLX has been confirmed by the sequence analysis of full-length ASPV genomic sequences available in the databases. In fact, a phylogenetic study based on a partial CP N-terminal sequence previously proposed to be involved in host adaptation has shown that ASPV-SL61 loquat isolate is more closely related to ASPV pear isolates. …”
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Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a forage breeding program by Sserumaga, J.P., Kayondo, S.I., Kigozi, A., Kiggundu, A., Namazzi, C., Walusimbi, K., Bugeza, J., Molly, A., Mugerwa, S.

“…Most orphan crops have not been fully sequenced, hence we rely on genome sequences of related species to align markers to different chromosomes. …”
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Using multiplex amplicon PCR technology to efficiently and timely generate Rift Valley fever virus sequence data for genomic surveillance by Juma, John, Konongoi, Samson L., Nsengimana, I., Mwangi, Reuben, Akoko, James M., Nyamota, Richard, Muli, Collins, Dobi, Paul O., Kiritu, Edward, Osiany, Shebbar, Onwong’a, A.A., Gachogo, R.W., Sang, R., Christoffels, A., Roesel, Kristina, Bett, Bernard K., Oyola, Samuel O.

“…It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. …”
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Genome edited wheat- current advances for the second green revolution by Awan, Muhammad Jawad Akbar, Pervaiz, Komal, Rasheed, Awais, Amin, Imran, Saeed, Nasir A., Dhugga, Kanwarpal S., Mansoor, Shahid

“…With the availability of reference genome sequence of wheat and advancement of allied genomics technologies, understanding of genes involved in grain yield components and disease resistance/susceptibility has opened new avenues for crop improvement. …”
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Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis by Asmare, Sisay, Alemayehu, Kefyalew, Mwacharo, Joram, Haile, Aynalem, Guangul, Solomon, Ahbara, Abulgasim

“…The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. …”
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Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens by Getachew, Fasil, Derks, M.F.L., Dessie, Tadelle, Hanotte, Olivier H., Barros, C.P., Crooijmans, R.P.M.A., Komen, H., Bastiaansen, J.W.M.

“…Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6–7 populations per gradient). …”
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Genome characterization of Rift Valley fever virus isolated from cattle, goats and sheep during interepidemic periods in Kenya by Onwong'a, A.A., Oyola, Samuel O., Juma, John, Konongoi, S., Nyamota, Richard, Mwangi, Reuben, Muli, Collins, Dobi, Paul, Bett, Bernard K., Ongus, J.R.

“…Two samples, 201808HABDVS from sheep and 201810CML3DVS from cattle, had Ct values of less than 20.0 and yielded whole genome sequences with 96.8 and 96.4 coverage, respectively. …”
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Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean by Zhang, Hailin, Fechete, Lavinia, Himmelbach, Axel, Poehlein, Anja, Lohwasser, Ulrike, Börner, Andreas, Maalouf, Fouad, Agrawal, Shiv Kumar, Khazaei, Hamid, Stein, Nils, Jayakodi, Murukarthick

“…Genotyping-by-sequencing (GBS) offers high-resolution genotyping for both model and crop plant species, even without a reference genome sequence. The genome fragments targeted by GBS depend substantially on the restriction enzyme (RE) used for the complexity reduction step. …”
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Fine mapping of a quantitative trait locus for spikelet number per panicle in a new plant type rice and evaluation of a near-isogenic line for grain productivity by Sasaki, Kazuhiro, Fujita, Daisuke, Koide, Yohei, Lumanglas, Patrick D., Gannaban, Ritchel B., Tagle, Analiza G., Obara, Mitsuhiro, Fukuta, Yoshimichi, Kobayashi, Nobuya, Ishimaru, Tsutomu

“…Fine mapping of qTSN12.2 revealed six candidate genes in a 92-kb region of the Nipponbare reference genome sequence between flanking markers RM28746 and RM28753. …”
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Defining the genome structure of ‘tongil’ rice, an important cultivar in the korean “green revolution by Kim, Backki, Kim, Dong-Gwan, Lee, Gileung, Seo, Jeonghwan, Choi, Ik-Young, Choi, Beom-Soon, Yang, Tae-Jin, Kim, Kwang Soo, Lee, Joohyun, Chin, Joong Hyoun, Koh, Hee-Jong

“…Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. …”
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Transposable element annotation of the rice genome by Juretic, Nikoleta, Bureau, Thomas E., Bruskiewich, Richard M.

“…Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. …”
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Cloning and genetic diversity analysis of a new P5CS gene from common bean (Phaseolus vulgaris L.) by Chen, J., Zhang, X., Jing, R, Blair, Matthew W., Mao, X, Wang, S.

“…Abundant indel (insertion and deletion events) and SNP (single nucleotide polymorphisms) were found in the cloned PvP5CS2 genome sequence when comparing 24 cultivated and 3 wild common bean accessions and these in turn reflected aspects of common bean evolution. …”
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Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast by Pais, TM, Foulquié Moreno, Maria R., Hubmann, Georg, Duitama, Jorge, Swinnen, S, Goovaerts, A, Yang, Y., Dumortier, F, Thevelein, JM

“…We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. …”
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