Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken.

Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis () locus on the 20th chromosome results in increased endothelin-3 () gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the locus spanning both Dup1 and Dup2 regions and establish that the scenario is correct of the three possible scenarios of the complex chromosomal rearrangement.

Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation.

Skeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers.

Evidence for the loss of plasminogen receptor KT gene in chicken.

The loss of conserved genes has the potential to alter phenotypes drastically. Screening of vertebrate genomes for lineage-specific gene loss events has identified numerous natural knockouts associated with specific phenotypes. We provide evidence for the loss of a multi-exonic plasminogen receptor KT (PLGRKT) protein-encoding gene located on the Z chromosome in chicken.

The genome sequence of Mesua ferrea and comparative demographic histories of forest trees.

Mesua ferrea (Family: Calophyllaceae) is a tropical forest plant used for timber, biofuel, and traditional medicine. Colloquially, it is known as Nagkesar (Cobra saffron) and is the state flower of Tripura (India). In this study, we perform the whole-genome assembly of Mesua ferrea using ~180X coverage paired-end Illumina data.

Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals.

The CYP8B1 gene is known to catalyse reactions that determine the ratio of primary bile salts and the loss of this gene has recently been linked to lack of cholic acid in the bile of naked-mole rats, elephants and manatees using forward genomics approaches. We screened the CYP8B1 gene sequence of more than 200 species and test for relaxation of selection along each terminal branch. The need for retaining a functional copy of the CYP8B1 gene is established by the presence of a conserved open reading frame across most species screened in this study.