Search Results - "genome sequencing"

Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from southwest part of Bangladesh by Al-Emran, Hassan M., Hasan, Md. Shazid, Setu, Md. Ali Ahasan, Rahman, M. Shaminur, Ul Alam, Rubayet A. S. M., Sarkar, Shovon Lal, Islam, Md. Tanvir, Islam, Mir Raihanul, Rahman, Mohammad Mahfuzur, Islam, Ovinu Kibria, Jahid, Iqbal Kabir, Hossain, M. Anwar

“…A total of 63 spike protein sequences and 14 whole-genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared. …”
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Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes by Gilbert, C., Meik, J.M., Dashevsky, D., Card, D.C., Castoe, T.A., Schaack, Sarah

“…We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii , the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. …”
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Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution by Palmenberg, A.C., Spiro, D., Kuzmickas, R., Wang, S., Djikeng, Appolinaire, Rathe, J.A., Fraser-Liggett, C.M., Liggett, S.B.

“…We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. …”
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Unravelling the genetic basis of banana traits using next generation sequencing technologies by Bioversity International

“…The availability of the banana reference genome sequence (D’Hont et al., 2012) and Next Generation Sequencing technologies have boosted research that helps to better understand the banana (Musa spp.) genetic diversity held in the Bioversity International Musa Germplasm Transit Centre (ITC). …”
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The Genus Citrus by Talón, Manuel, Caruso, Marco, Gmitter Jr., Frederick G.

“…Reporting on new insights supported by the elucidation of the citrus genome sequence, it presents groundbreaking theories and fills in previous knowledge gaps. …”
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Whole genome assembly, annotation and bioinformatics analysis of Bacillus amyloliquefaciens strain UCMB5113" by Niazi, Adnan

“…The determination of draft genome sequence of UCMB5113 provided very basic analysis of set of genes involved in plant bacterium interaction and plant growth and protection. …”

Exploring genetic diversity and selection signatures in indigenous African cattle breeds by Friedrich, J., Bailey, R., Talenti, A., Marshall, Karen, Prendergast, J., Wiener, P.

“…We analysed whole-genome sequence data of over 100 African cattle comprising 9 breeds and calculated within- and between-breed population statistics to characterise genetic diversity and identify selection signatures. …”
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A structural variant at ASIP associated with the darkness of hair coat is found in multiple zebu cattle populations by Trigo, B.B., Alves, N.F., Milanesi, M., Garcia, J.F., Terefe, Endashaw, Hanotte, Olivier H., Tijjani, Abdulfatai, Utsunomiya, Y.T.

“…Here we visually analyzed the whole‐genome sequence of zebu and taurine (Bos taurus) cattle to elucidate the extent of spread of ASIP‐SV1 in different cattle populations. …”
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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice by Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F., Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D., Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A.

“…Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. …”
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Genome characterization of three potyviruses affecting maize in Argentina by Trucco, Veronica Milagros, Cabrera Mederos, Dariel, Castellanos Collazo, Onias, Vaghi Medina, Carlos Gaston, Lenardon, Sergio Luis, Giolitti, Fabian

“…The results of this work are the first data in Argentina of complete genome sequences of potyviruses obtained from maize and the first obtained for JGMV and MDMV.…”
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Citrus Genomics and Breeding: Identification of Candidate Genes by the Use of Mutants and Microarrays by Talón, Manuel, Cercós, Manuel, Iglesias, Domingo J., Colmenero-Flores, José M., Ibanez, Victoria, Brumos, Javier, Herrero-Ortega, Amparo, Ríos, Gabino, Terol, Javier, Tadeo, Francisco R.

“…This goal is supported by two complementary strategies the identification of genes of agricultural interest by the use of mutants and microarrays and the elucidation of the citrus genome sequence. In this communication the efforts we are developing in this first approach are revised while the other strategy will be resumed elsewhere.…”
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Review of empirical and emerging breeding methods and tools for yam (Dioscorea spp.) improvement: status and prospects by Darkwa, K., Olasanmi, B., Asiedu, R., Asfaw, A.

“…Substantial efforts have also been made to develop diverse molecular markers, transcriptome and metabolome profiles of crucial traits, trait mapping and generate reference genome sequences of the key species. However, there seems to be a slow translation of research improvements into widespread applications. …”
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The lowest hanging fruit: Beneficial gene knockouts in past, present, and future crop evolution by Monroe, J.G., Arciniegas Vega, Juan Pablo, Moreno, J.L., Sánchez, F., Sierra, S., Valdés, S., Torkamaneh, D., Chavarriaga, P.

“…Recent advances in the generation of whole genome sequence data and functional investigations into the molecular genetic basis of crop traits continue to reveal the existence of considerable beneficial loss of function in crop species. …”
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Improvement of nutraceutical traits of banana: new breeding techniques by Tripathi, J., Ntui, V.O., Malarvizhi, M., Muiruri, K.S., Ravishankar, K., Tripathi, L.

“…Accessibility of well-annotated Musa genome sequences and established transformation and gene-editing platforms can contribute to developing banana with high dietary value. …”
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Using the transcriptome to annotate the genome revisited: application of massively parallel signature sequencing (MPSS) by Shah, Tushaar, Villiers, Etienne P. de, Nene, Vishvanath M., Hass, B., Taracha, E.A., Gardner, J.M., Sansom, C., Pelle, Roger, Bishop, Richard P.

“…Transcriptome analysis can provide useful data for refining genome sequence annotation. Application of massively parallel signature sequencing (MPSS) revealed reproducible transcription, in multiple MPSS cycles, from 73% of computationally predicted genes in the Theileria parva schizont lifecycle stage. …”
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The International Rice Information System. A platform for meta-analysis of rice crop data by McLaren, Christopher Graham, Bruskiewich, Richard M., Portugal, Arllet M., Cosico, Alexander B.

“…New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. …”
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Characterisation of single domain ATP-binding cassette protein homologues of Theileria parva by Kibe, M.K., Macklin, M.D., Gobright, E.I., Bishop, Richard P., Urakawa, T., Ole-MoiYoi, O.K.

“…Comparison of cDNA and genomic sequences revealed that TpABCl contained seven short introns, between 29 and 84 bp in length. …”
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Highre-solution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations by International Cassava Genetic Map Consortium

“…The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selectionenhanced breeding of this important crop.…”
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Chromosome evolution and the genetic basis of agronomically important traits in greater yam by Bredeson, J.V., Lyons, J.B., Oniyinde, I.O., Okereke, N.R., Kolade, O., Nnabue, I., Nwadili, C.O., Hřibová, E., Parker, M., Nwogha, J., Shu, S., Carlson, J., Kariba, R., Muthemba, S., Knop, K., Barton, G.J., Sherwood, A.V., López Montes, A., Asiedu, R., Jamnadass, Ramni, Muchugi, A., Goodstein, D., Egesi, Chiedozie N., Featherston, J., Asfaw, A., Simpson, G.G., Doležel, J., Hendre, P.S., Deynze, A. van, Kumar, P. Lava, Obidiegwu, J.E., Bhattacharjee, Ranjana, Rokhsar, D.S.

“…Here we address this resource gap by presenting a highly-contiguous chromosome-scale genome assembly of greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. …”
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Shaping the future of bananas: advancing genetic trait regulation and breeding in the post-genomics era by Miao, Hongxia, Zhang, Jianbin, Zheng, Yunke, Jia, Caihong, Hu, Yulin, Wang, Jingyi, Zhang, Jing, Sun, Peiguang, Jin, Zhiqiang, Zhou, Yongfeng, Zheng, Sijun, Wang, Wei, Rouard, Mathieu, Xie, Jianghui, Liu, Juhua

“…Following the publication of complete A- and B-genome sequences, prospects for complementary studies on S- and T-genome traits, key gene identification for yield, ripening, quality, and stress resistance, and advances in molecular breeding have significantly expanded. …”
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