Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data
Sign Up to like & getrecommendations! Published in 2019 at "Science China Life Sciences"
DOI: 10.1007/s11427-019-9551-7
Abstract: Pigs were domesticated independently in the Near East and China, indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide. Therefore, 12 de… read more here.
Keywords: building sequence; pan genome; pig; reference genome ... See more keywords
The chromosome-level reference genome of Coptischinensis provides insights into genomic evolution and berberine biosynthesis
Sign Up to like & getrecommendations! Published in 2021 at "Horticulture Research"
DOI: 10.1038/s41438-021-00559-2
Abstract: Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis has been used as a traditional medicine for more than 2000 years in China and many other Asian… read more here.
Keywords: reference genome; level; chinensis; chromosome level ... See more keywords
Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing
Sign Up to like & getrecommendations! Published in 2019 at "Human Genome Variation"
DOI: 10.1038/s41439-019-0057-7
Abstract: In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented.… read more here.
Keywords: single molecule; reference genome; molecule real; reference ... See more keywords
The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins
Sign Up to like & getrecommendations! Published in 2020 at "Nature Genetics"
DOI: 10.1038/s41588-019-0559-8
Abstract: Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome… read more here.
Keywords: cobra; reference genome; venom; genome transcriptome ... See more keywords
Extended regions of suspected mis-assembly in the rat reference genome
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Data"
DOI: 10.1038/s41597-019-0041-6
Abstract: We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to… read more here.
Keywords: rat reference; reference genome; regions suspected; genome ... See more keywords
A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-34812-x
Abstract: Leishmania donovani is responsible for visceral leishmaniasis, a neglected and lethal parasitic disease with limited treatment options and no vaccine. The study of L. donovani has been hindered by the lack of a high-quality reference… read more here.
Keywords: virulence; reference genome; leishmania donovani; donovani ... See more keywords
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
Sign Up to like & getrecommendations! Published in 2021 at "Communications Biology"
DOI: 10.1038/s42003-021-01698-x
Abstract: We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1%… read more here.
Keywords: reference; novel canine; reference genome; dog ... See more keywords
AStrap: identification of alternative splicing from transcript sequences without a reference genome
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty1008
Abstract: Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de… read more here.
Keywords: reference genome; transcript sequences; reference; astrap ... See more keywords
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)
Sign Up to like & getrecommendations! Published in 2021 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evab029
Abstract: Abstract From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic… read more here.
Keywords: reference genome; biology; high quality; quality reference ... See more keywords
De novo assembly of the cattle reference genome with single-molecule sequencing
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DOI: 10.1093/gigascience/giaa021
Abstract: Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was… read more here.
Keywords: novo assembly; reference genome; cattle reference; reference ... See more keywords
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome
Sign Up to like & getrecommendations! Published in 2022 at "GigaScience"
DOI: 10.1093/gigascience/giab096
Abstract: Abstract Background The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms… read more here.
Keywords: reference genome; genome assembly; functional annotation; genome ... See more keywords