Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
JL Fierst - Frontiers in genetics, 2015 - frontiersin.org
Modern high-throughput DNA sequencing has made it possible to inexpensively produce
genome sequences, but in practice many of these draft genomes are fragmented and …
genome sequences, but in practice many of these draft genomes are fragmented and …
Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching
INTRODUCTION Coral reefs worldwide are suffering losses at an alarming rate as a result of
anthropogenic climate change. Increased seawater temperatures, even only slightly above …
anthropogenic climate change. Increased seawater temperatures, even only slightly above …
A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana
Demand for cannabidiol (CBD), the predominant cannabinoid in hemp (Cannabis sativa),
has favored cultivars producing unprecedented quantities of CBD. We investigated the …
has favored cultivars producing unprecedented quantities of CBD. We investigated the …
Between two fern genomes
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear
genome. This lack of genome sequence information significantly impedes our ability to …
genome. This lack of genome sequence information significantly impedes our ability to …
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By
combining high-throughput sequencing, recent developments in parallel computing, and …
combining high-throughput sequencing, recent developments in parallel computing, and …
Extensive error in the number of genes inferred from draft genome assemblies
JF Denton, J Lugo-Martinez, AE Tucker… - PLoS computational …, 2014 - journals.plos.org
Current sequencing methods produce large amounts of data, but genome assemblies based
on these data are often woefully incomplete. These incomplete and error-filled assemblies …
on these data are often woefully incomplete. These incomplete and error-filled assemblies …
Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods
Background Recent advances in genomics indicate functional significance of a majority of
genome sequences and their long range interactions. As a detailed examination of genome …
genome sequences and their long range interactions. As a detailed examination of genome …
The time scale of recombination rate evolution in great apes
We present three linkage-disequilibrium (LD)-based recombination maps generated using
whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western …
whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western …
Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe
JK Olofsson, I Cantera, C Van de Paer… - Molecular ecology …, 2019 - Wiley Online Library
Species trees have traditionally been inferred from a few selected markers, and genome‐
wide investigations remain largely restricted to model organisms or small groups of species …
wide investigations remain largely restricted to model organisms or small groups of species …
The relevance of pedigrees in the conservation genomics era
SJ Galla, L Brown, Y Couch‐Lewis, I Cubrinovska… - 2022 - Wiley Online Library
Over the past 50 years conservation genetics has developed a substantive toolbox to inform
species management. One of the most long‐standing tools available to manage genetics …
species management. One of the most long‐standing tools available to manage genetics …