An Effective Preprocessing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1720-5_21
Abstract: Bacillus subtilis and Escherichia coli, as widely used microbial species, are of great significance in studying microbial community relationships, adaptive evolution in various niches, engineering cell factories that produce specific products, and designing genome reduction.… read more here.
Keywords: quality; pan genome; quality pan; high quality ... See more keywords
Prospects of pan-genomics in barley
Sign Up to like & getrecommendations! Published in 2018 at "Theoretical and Applied Genetics"
DOI: 10.1007/s00122-018-3234-z
Abstract: The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover… read more here.
Keywords: pan genomics; barley; pan genome; genetics ... See more keywords
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
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Sign Up to like & getrecommendations! Published in 2021 at "Cell"
DOI: 10.1016/j.cell.2021.04.046
Abstract: Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed… read more here.
Keywords: rice; diverse rice; genomic variations; pan genome ... See more keywords
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Sign Up to like & getrecommendations! Published in 2022 at "Nature Communications"
DOI: 10.1038/s41467-022-28362-0
Abstract: Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber ( Cucumis sativus L.) have been hindered… read more here.
Keywords: graph based; cucumber; based pan; agronomic traits ... See more keywords
Pan-genome upgrade
Sign Up to like & getrecommendations! Published in 2020 at "Nature Plants"
DOI: 10.1038/s41477-020-0731-2
Abstract: Thanks to the advances of sequencing technologies, pan-genomes can now be assembled to capture the full genetic diversity of a certain species. A soybean pan-genome based on seven wild accessions was assembled with short reads… read more here.
Keywords: graph based; diversity; pan genome; genome upgrade ... See more keywords
Extensive variation within the pan-genome of cultivated and wild sorghum.
Sign Up to like & getrecommendations! Published in 2021 at "Nature plants"
DOI: 10.1038/s41477-021-00925-x
Abstract: Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its… read more here.
Keywords: variation; pan genome; within pan; sorghum ... See more keywords
Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.).
Sign Up to like & getrecommendations! Published in 2021 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2105431118
Abstract: Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here,… read more here.
Keywords: pan genome; history; fragaria spp; strawberry fragaria ... See more keywords
EUPAN enables pan‐genome studies of a large number of eukaryotic genomes
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx170
Abstract: Summary: Pan‐genome analyses are routinely carried out for bacteria to interpret the within‐species gene presence/absence variations (PAVs). However, pan‐genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes.… read more here.
Keywords: pan genome; genome analyses; eupan enables; genome ... See more keywords
ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz168
Abstract: SUMMARY Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics.… read more here.
Keywords: absence variants; pipeline; pan genome; presence absence ... See more keywords
Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources
Sign Up to like & getrecommendations! Published in 2023 at "Genetics"
DOI: 10.1093/genetics/iyac191
Abstract: Abstract As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture,… read more here.
Keywords: genome database; saccharomyces genome; database update; pan genome ... See more keywords