Results 91 to 100 of about 48,352 (276)

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

Nature Communications
Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together.
Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M. Devaney, Jessica Noya, April S. Berlyoung, Rhonda Brandon, Kathleen S. Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, UCI Genomics Research to Elucidate the Genetics of Rare diseases (UCI GREGoR) Consortium, Michael A. Eberle   +22 more
doaj   +1 more source

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution [PDF]

, 2018
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P.
Arnathau, Céline, Boundenga, Larson, Durand, Patrick, Franzon, Blaise, Gilabert, Aude, Makanga, Boris, Moukodoum, Nancy D., Ngoubangoye, Barthélémy, Okouga, Alain-Prince, Ollomo, Benjamin, Otto, Thomas D., Paupy, Christophe, Prugnolle, Franck, Renaud, François, Rougeron, Virginie, Rutledge, Gavin G.   +15 more
core   +5 more sources

Improve homology search sensitivity of PacBio data by correcting frameshifts [PDF]

Bioinformatics, 2016
Single-molecule, real-time sequencing developed by Pacific BioSciences produces longer reads than secondary generation sequencing technologies such as Illumina. However, PacBio data has high sequencing error rate and most of the errors are insertion or deletion errors, causing frameshifts and leading to marginal alignment scores and short alignments in
Nan, Du, Yanni, Sun
openaire   +2 more sources

Gene turnover in the common ancestor of all C4 grasses

PLANTS, PEOPLE, PLANET, EarlyView.
Understanding how plants evolve more efficient photosynthesis is important in a warming world where improving crop productivity and resilience is a global priority. By generating the first reference genomes for an early‐diverging group of grasses called the Aristidoideae, we were able to reconstruct the genetic makeup of the last common ancestor of all
Lara Pereira, Ahmed S. Alenazi, Sahr Mian, Ilia J. Leitch, Pascal‐Antoine Christin, Colin P. Osborne, Luke T. Dunning   +6 more
wiley   +1 more source

Soil Metagenome PacBio v1

This protocol describes the sample collection to sequence acquisition workflow for PacBio Revio long-read sequencing of a complex soil sample using SMRT Bell library prep kit 2.0 and Revio SMRT cells.
Robert S James, Gaetan Benoit, Sebastian Raguideau, Georgina Alabone, Christopher Quince   +4 more
openaire   +1 more source

From wild to tamed: Reimagining novel crops through omics and local plant diversity

PLANTS, PEOPLE, PLANET, EarlyView.
The global food system faces growing pressure from climate change, biodiversity loss, and rising nutritional demands. Agriculture has increased yields but reduced crop diversity, flavor, and nutritional quality, leaving societies vulnerable and dependent on a narrow set of staple species.
Alexandra Sanfeliu Meliá, Pablo D. Cárdenas   +1 more
wiley   +1 more source

Cerulean: A hybrid assembly using high throughput short and long reads

, 2013
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions.
D.R. Zerbino, E.W. Myers, E.W. Myers, F.J. Ribeiro, J. Schmutz, J.T. Simpson, J.T. Simpson, M. Eisenstein, M.J. Chaisson, M.J. Chaisson, P.A. Pevzner, R. Staden, R.M. Idury, S. Koren, T.D. Wu   +14 more
core   +1 more source

First genome sequence of a European Alternaria brassicae isolate and genes involved in early development of alternaria leaf spot on Brassica juncea

Pest Management Science, EarlyView.
This article reports the first genome sequence of a UK Alternaria brassicae isolate. Dual RNA‐sequencing profiling of A. brassicae‐infected Brassica juncea leaves identified differentially expressed genes involved in pathogenicity and host response pathways in moderately resistant Sej‐2 (2) and moderately susceptible Pusa Jaikisan cultivars.
Kevin M. King, Graham McLaughlin, Chinthani S. Karandeni Dewage, Zedi Gao, David J. Hughes, Jonathan S. West, Henrik U. Stotz   +6 more
wiley   +1 more source

Improving PacBio Long Read Accuracy by Short Read Alignment

PLoS ONE, 2012
The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies.
Kin Fai Au, Jason G Underwood, Lawrence Lee, Wing Hung Wong   +3 more
openaire   +4 more sources

Full‐length transcriptome profiling of true bug mitochondrial genomes reveals the unique transcriptional regulation during insect evolution

Insect Science, EarlyView.
The mitogenome was transcribed into complete primary polycistrons on both strands. The heteropteran mitochondrial transcription termination factor (HmTTF) functions as a bidirectional attenuator rather than a terminator, and co‐evolution of HmTTF and the binding sites was observed.
Shiwen Xu, Yuange Duan, Ling Ma, Qiaoqiao Liu, Fan Song, Wanzhi Cai, Hu Li   +6 more
wiley   +1 more source