Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data
Construction of chromosome-level assembly is a vital step in achieving the goal of a
'Platinum'genome, but it remains a major challenge to assemble and anchor sequences to …
'Platinum'genome, but it remains a major challenge to assemble and anchor sequences to …
De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana
T Xie, JF Zheng, S Liu, C Peng, YM Zhou, QY Yang… - Molecular plant, 2015 - cell.com
Genome assembly is typically a two-stage process: paired sequencing reads are joined into
contigs, and contigs are assembled into scaffolds. Over the past 10 years, next-generation …
contigs, and contigs are assembled into scaffolds. Over the past 10 years, next-generation …
Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes
FA Rabanal, M Gräff, C Lanz, K Fritschi… - Nucleic Acids …, 2022 - academic.oup.com
Although long-read sequencing can often enable chromosome-level reconstruction of
genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model …
genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model …
YaHS: yet another Hi-C scaffolding tool
C Zhou, SA McCarthy, R Durbin - Bioinformatics, 2023 - academic.oup.com
We present YaHS, a user-friendly command-line tool for the construction of chromosome-
scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal …
scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal …
Building near-complete plant genomes
TP Michael, R VanBuren - Current Opinion in Plant Biology, 2020 - Elsevier
Highlights•Long read sequencing has improved genome assembly by an order of
magnitude.•New genome assembly algorithms leverage long, error prone reads to untangle …
magnitude.•New genome assembly algorithms leverage long, error prone reads to untangle …
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish
microbial genomes, but available assembly methods have not scaled well to larger …
microbial genomes, but available assembly methods have not scaled well to larger …
Phased diploid genome assembly with single-molecule real-time sequencing
While genome assembly projects have been successful in many haploid and inbred
species, the assembly of noninbred or rearranged heterozygous genomes remains a major …
species, the assembly of noninbred or rearranged heterozygous genomes remains a major …
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis
S Akama, R Shimizu-Inatsugi, KK Shimizu… - Nucleic acids …, 2014 - academic.oup.com
Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants,
and is considered to be a strong force for generating new species. However, genome-wide …
and is considered to be a strong force for generating new species. However, genome-wide …
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It
is commonly used as a vegetable and medicinal herb because of its excellent nutritional …
is commonly used as a vegetable and medicinal herb because of its excellent nutritional …
Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly
D Yin, C Ji, X Ma, H Li, W Zhang, S Li, F Liu… - …, 2018 - academic.oup.com
Abstract Arachis monticola (2n= 4x= 40) is the only allotetraploid wild peanut within the
Arachis genus and section, with an AABB-type genome of∼ 2.7 Gb in size. The AA-type …
Arachis genus and section, with an AABB-type genome of∼ 2.7 Gb in size. The AA-type …