Huang, X.-H. | Search bioRxiv

bioRxiv2024

Two distinct structural variants involving EDN3 cause hyperpigmentation in chicken

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant causing upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed structural arrangement and functional consequences of the variant remained unclear. In this study, we conducted a comprehensive genomic survey of 692 FM chickens representing 55 breeds and uncovered two distinct structural variants causing the FM phenotype: FM*A, the previously reported complex rearrangement involving the EDN3 locus1, and FM*B, a tandem duplication of a 16 kb region upstream of EDN3. We demonstrate that both structural variants (SVs) significantly upregulate EDN3 expression, with FM*B associated with even higher expression than FM*A. A luciferase reporter assays showed that the 16 kb region in FM*B contains powerful enhancers and the copy number expansion of this element is a likely explanation for EDN3 upregulation and hyperpigmentation. Furthermore, our analysis of linkage disequilibrium patterns allowed us to resolve the complex arrangement of duplications and inversion on the FM*A haplotype.

genomics↗

bioRxiv2022

Chlamydomonas mutant hpm91 lacking PGR5 is a scalable and valuable strain for algal hydrogen (H2) production

Clean and sustainable H2 production is essential toward a carbon-neutral world. H2 generation by Chlamydomonas reinhardtii is an attractive approach for solar-H2 from H2O. However, it is currently not scalable because of lacking ideal strains. Here, we explore hpm91, a previously reported PGR5-deletion mutant with remarkable H2 production, that possesses numerous valuable attributes towards large-scale application and in-depth study issues. We show that hpm91 is at least 100-fold scalable (upto 10 liter) with H2 collection sustained for averagely 26 days and 7287 ml H2/10L-HPBR. Also, hpm91 is robust and active over the period of sulfur-deprived H2 production, most likely due to decreased intracellular ROS relative to wild type. Moreover, quantitative proteomic analysis revealed its features in photosynthetic antenna, primary metabolic pathways and anti-ROS responses. Together with success of new high-H2-production strains derived from hpm91, we highlight that hpm91 is a potent strain toward basic and applied research of algal-H2 photoproduction.

biochemistry↗