https://orcid.org/0000-0002-3752-0654vhtechio@ufla.brVnia Helena TechioView further author informationhttps://orcid.org/0000-0003-3054-5127Cacilda Borges Do ValleView further author informationhttps://orcid.org/0000-0002-5490-4959Sanzio Carvalho Lima Barrios...
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome sequence of an organism from sequencing reads — has been a central problem in bioinformatics for four decades. Until recently, genomes were typical...
In a typical genome, a highly contiguous assembly could be organized (‘scaffolded’) into chromosomes solely by Hi-C or optical mapping; however, both of these technologies require short unique sequence anchors, which are rare in the R570 genome. Therefore scaffolding required a custom pipeline ...
“Traditionally sugarcane has been bred just for sugar but now with the move to net zero, there is great interest in one of the most productive crops in the world becoming a source of renewable carbon,” he said. “This genome mapping will help us produce sugarcane that’s a better raw ...
(ref.92). The linkage mapping was conducted with Lep-MAP3 (ref.83). The markers were clustered into paternal and maternal linkage groups by using a logarithm of the odds score of 18 in a segregation distortion aware model. The final curation of the assembly, combining the two parental ...
In cotton, there are several reports on the molecular regulatory mechanisms that orchestrate drought resistance using quantitative trait loci (QTL) mapping or by developing drought stress induced cDNA libraries [28–30]. In addition, microarray gene expression profiling has been used in cotton tissues...
The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nat Genet. 2019;51(5):865–76. 23. Clevenger J, Chu Y, Scheffler B, Ozias-Akins P. A developmental transcriptome map for allotetraploid Arachis hypogaea. Front Plant Sci. 2016;...
genome ofM. acuminatawould provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivatedMusapolyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding ...
ofNicotianaallopolyploids found that five million years after the WGD event, the two parental genomes in the polyploid were no longer distinguishable due to genome turnover, mutations, and small-scale duplications59. However, our BAC-FISH results further corroborated our sequencing results in ...
The analysis of K-mer spectra confirmed the limited residual heterozygosity of the 2C breeding line; this was markedly lower than the levels detected in the parental genotypes (globe artichoke and cultivated cardoon) of our mapping population (see below; Supplementary Fig. S1). Based on K-mer...