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T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. sativa L.)
BackgroundThe Arabidopsis DA1 gene is a key player in the regulation of organ and seed development. To extend our understanding of its functional...
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Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog
BackgroundIn eukaryote transcriptomes, a significant amount of transcript diversity comes from genes’ capacity to generate different transcripts...
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Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human
The African grass or Nile rat (NR) ( Arvicanthis niloticus ) is a herbivorous diurnal rodent which is used as a biological model for research on type 2...
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Expression and Functional Studies of Leaf, Floral, and Fruit Developmental Genes in Non-model Species
Researchers working on evolutionary developmental plant biology are inclined to choose non-model taxa to address how specific features have been...
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Protein-Coding Gene Families in Prokaryote Genome Comparisons
The identification of orthologous genes is relevant for comparative genomics, phylogenetic analysis, and functional annotation. There are many...
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Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean
BackgroundMung bean ( Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous...
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Regulation of Seed Dormancy Genes in Triticeae Species
Wild progenitors of Triticeae crops generally have long dormancy periods. Domesticated crops inherited these longer dormancy alleles from their wild...
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Genes divided according to the relative position of the longest intron show increased representation in different KEGG pathways
Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and...
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Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt
BackgroundMost disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS)...
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Employing protein size in the functional analysis of orthologous proteins, as illustrated with the yeast HOG pathway
Comparative genomics has provided us with a new handle on the interpretation of protein sequences. The sequencing of numerous fungal genomes has...
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Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes
The Aryl hydrocarbon receptor is an ancient transcriptional factor originally discovered as a sensor of dioxin. In addition to its function as a...
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Genome-wide characterization and expression of Oryza sativa AP2 transcription factor genes associated with the metabolism of mesotrione
BackgroundThe APETALA2 (AP2) transcription factor (TF) superfamily, one of the largest gene families in plants, plays an essential role in regulating...
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QTL and Candidate Genes for Flax Disease Resistance
Rust, pasmo (PAS), powdery mildew (PM), and Fusarium wilt (FW) are four major diseases of flax, causing yield losses as well as seed and fiber...
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Identification and expression analyses of B3 genes reveal lineage-specific evolution and potential roles of REM genes in pepper
BackgroundThe B3 gene family, one of the largest plant-specific transcription factors, plays important roles in plant growth, seed development, and...
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Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae
BackgroundThe AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and...
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A standardized nomenclature for mammalian histone genes
Histones have a long history of research in a wide range of species, leaving a legacy of complex nomenclature in the literature. Community-led...
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Finding functional associations between prokaryotic virus orthologous groups: a proof of concept
BackgroundThe field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery....
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Insights of auxin signaling F-box genes in wheat (Triticum aestivum L.) and their dynamic expression during the leaf rust infection
The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading...
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Genome-wide bioinformatics analysis reveals the evolutionary origin of BnGRAS genes in the Brassica genus
As important plant-specific transcription factors, GRAS family members play significant roles in plant development and diverse stress responses. The...
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Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species
BackgroundGenes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses....
