[HTML][HTML] Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes
Comparisons of genomes of different species are used to identify lineage-specific genes,
those genes that appear unique to one species or clade. Lineage-specific genes are often …
those genes that appear unique to one species or clade. Lineage-specific genes are often …
[HTML][HTML] The lost and found: unraveling the functions of orphan genes
Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant
attention. Despite lacking a clear evolutionary history, they are found in nearly all living …
attention. Despite lacking a clear evolutionary history, they are found in nearly all living …
The ORFans' tale: new insights in plant biology
Orphan genes (OGs) are protein-coding genes without a significant sequence similarity in
closely related species. Despite their functional importance, very little is known about the …
closely related species. Despite their functional importance, very little is known about the …
Critical assessment of pan-genomic analysis of metagenome-assembled genomes
T Li, Y Yin - Briefings in Bioinformatics, 2022 - academic.oup.com
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the
known issues with MAGs: fragmentation, incompleteness and contamination. Here, we …
known issues with MAGs: fragmentation, incompleteness and contamination. Here, we …
Bioinformatics identification of anti-CRISPR loci by using homology, guilt-by-association, and CRISPR self-targeting spacer approaches
Y Yin, B Yang, S Entwistle - Msystems, 2019 - Am Soc Microbiol
ABSTRACT Anti-CRISPR (Acr) loci/operons encode Acr proteins and Acr-associated (Aca)
proteins. Forty-five Acr families have been experimentally characterized inhibiting seven …
proteins. Forty-five Acr families have been experimentally characterized inhibiting seven …
Distinct but intertwined evolutionary histories of multiple Salmonella enterica subspecies
Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid)
fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and …
fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and …
Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences
WM Karlowski, D Varshney… - Genome Biology and …, 2023 - academic.oup.com
Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and
may act as potential genetic determinants of lineage-specific, biological properties. Here, we …
may act as potential genetic determinants of lineage-specific, biological properties. Here, we …
[HTML][HTML] AtQQS orphan gene and NtNF-YC4 boost protein accumulation and pest resistance in tobacco (Nicotiana tabacum)
Abstract Qua-Quine Starch (QQS), an orphan gene exclusively found in Arabidopsis
thaliana, interacts with Nuclear Factor Y subunit C4 (NF-YC4) and regulates carbon and …
thaliana, interacts with Nuclear Factor Y subunit C4 (NF-YC4) and regulates carbon and …
Polyphenol utilization proteins in the human gut microbiome
Dietary polyphenols can significantly benefit human health, but their bioavailability is
metabolically controlled by human gut microbiota. To facilitate the study of polyphenol …
metabolically controlled by human gut microbiota. To facilitate the study of polyphenol …
Distinct genome trichotomy in members of Hapalosiphonaceae is guided by habitat adaptation with Mastigocladus laminosus UU774 as a case study
A Geeta, M Mukherjee, B Das, S Dutta, A Prusty… - Algal Research, 2024 - Elsevier
The family Hapalosiphonaceae is grouped under subsection IV complying with International
Code of Nomenclature for algae, fungi, and plants (ICN). This is a complex taxonomic group …
Code of Nomenclature for algae, fungi, and plants (ICN). This is a complex taxonomic group …