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Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 mi...


Fuentes, Roven RommelChebotarov, DmytroDuitama, JorgeSmith, SeanHoz, Juan Fernando de laMohiyuddin, MarghoobWing, Rod A.McNally, Kenneth L.Tatarinova, TatianaGrigoriev, AndreyMauleon, RamilAlexandrov, Nickolai[Structural variants in 3000 rice genomes]Structural variants in 3000 rice genomes

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this s...


Silva, G.Bömer, M.Rathnayake, A.I.Sewe, S.O.Visendi, P.Oyekanmi, J.O.Quain, M.D.Akomeah, B.Kumar, P.L.Seal, S.E.[Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing]Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing

Na+ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under var...


Kumari, P.H.Kumar, S.A.Ramesh, K.Reddy, P.S.Nagaraju, M.Prakash, A.B.Shah, T.Henderson, A.Srivastava, R.K.Rajasheker, G.Chitikineni, A.Varshney, Rajeev K.Rathnagiri, P.Narasu, M.L.Kishor, P.B.K.[Genome-wide identification and analysis of arabidopsis sodium proton antiporter (NHX) and human sodium proton exchanger (NHE) homologs in sorghum bicolor]Genome-wide identification and analysis of arabidopsis sodium proton antiporter (NHX) and human sodium proton exchanger (NHE) homologs in sorghum bicolor

The complete bipartite genome (RNA1 and RNA2) of a new nepovirus infecting potato was obtained using small RNA sequencing and assembly complemented by Sanger sequencing. Each RNA encodes a single polyprotein, flanked by 5’ and 3’ untranslate regions (UTR) and followed by a poly (A) tail. The puta...


Souza, Joao deMuller, G.Pérez, W.Cuéllar, Wilmer J.Kreuze, J.F.[Complete sequence and variability of a new subgroup B nepovirus infecting potato in central Peru]Complete sequence and variability of a new subgroup B nepovirus infecting potato in central Peru

Artificial miRNAs (amiRNA) were generated targeting conserved sequences within the genomes of the two causal agents of Cassava brown streak disease (CBSD): Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Transient expression studies on ten amiRNAs targeting 21 nt...


Wagaba, HenryPatil, Basavaprabhu L.Mukasa, SettumbaAlicai, TitusFauquet, Claude M.Taylor, Nigel J.[Artificial microRNA-derived resistance to Cassava brown streak disease]Artificial microRNA-derived resistance to Cassava brown streak disease

We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mut...


Morton, B.Vroh Bi, IrieMcMullen, M.Gaut, B.[Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.]Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.

Transgenic plant studies have lead to the breakthrough discovery of RNA silencing as a conserved mechanism for gene regulation across kingdoms. Recent molecular genetic studies have revealed a major role for RNA silencing in the formation of silent chromatin, characterized by histone modification...


Ingelbrecht, I.Mirkov, T.E.Dixon, Alfred G.O.Menkir, A.[Epigenetic lessons from transgenic plants In: Floricultural, ornamental and plant biotechnology: advances and topical issues]Epigenetic lessons from transgenic plants In: Floricultural, ornamental and plant biotechnology: advances and topical issues

The responses of 19 East African highland (EAH) banana cultivars (AAA and AA genomes) and two reference cultivars to black sigatoka (Mycosphaerella fijiensis Morelet) and Cladosporium leaf speckle (Cladosporium musae Mason) were studied in 1993 at Onne (southeastern Nigeria) under ecological cond...


Pasberg-Gauhl, C.Gauhl, F.[Response of East African highland bananas to black Sigatoka and Cladosporium leaf speckle under tropical humid forest lowland conditions in West Africa]Response of East African highland bananas to black Sigatoka and Cladosporium leaf speckle under tropical humid forest lowland conditions in West Africa

Sharma, S.K.Bolser, D.Boer, J. de.Sonderkaer, M.Amoros, W.Carboni, M.F.D'Ambrosio, J.M.Cruz, G. de laGenova, A. diDouches, D.S.Eguiluz, M.Guo, X.Guzmán, F.Hackett, C.A.Hamilton, J.P.Li, G.Li, Y.Lozano, R.Maass, A.Marshall, D.Martínez, D.McLean, K.Mejia, N.Milne, L.Munive, S.Nagy, I.Ponce, O.Ramírez, M.Simon, R.Thomson, S.J.Torres, Y.Waugh, R.Zhang, Z.Huang, S.Visser, Richard G.F.Bachem, C.W.B.Sagredo, B.Feingold, S.E.Orjeda, G.Veilleux, R.E.Bonierbale, Merideth W.Jacobs, J.M.E.Milbourne, D.Martin, D.M.A.Bryan, G.J.[Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps.]Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps.

Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and ...


Baurens, F.C.Martin, G.Hervouet, C.Salmon, F.Yohoume D.Ricci, S.Rouard, M.Habas, R.Yahiaoui, N.D’Hont, A.[Recombinations and large structural variations shape the mosaic genomes of interspecific edible bananas]Recombinations and large structural variations shape the mosaic genomes of interspecific edible bananas

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