Guang, Y. | bioRxiv Science

bioRxiv2024

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation

Rice (Oryza sativa) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous O. longistaminata genome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 343-Mb telomere-to-telomere (T2T) genome assembly for this species, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between the O. longistaminata and O. sativa. A total of 2,466 segmentally duplicated genes were identified and enriched in cellular amino acid metabolic processes. We detected a slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of O. longistaminata provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.

genomics↗

bioRxiv2019

Osmoregulation of glutamine synthetase from Giant freshwater prawn (Macrobrachium rosenbergii) under osmotic stress

Glutamine synthetase is a key enzyme that catalyzes the biosynthesis of glutamine (Gln) from glutamate and ammonia. Gln a vital amino acid acts as a precursor for protein synthesis and also assist in ammonia repressor and a key osmoregulators in aquatics. Here, we report the cloning and characterization of the GS gene from Macrobrachium rosenbergii (Mr-GS). The complete nucleotide and deduced amino acid sequences were determined that phylogenetically shared highest identity with other crustaceans. GS mRNA was differentially expressed in 6 different tissues, with high to low order as muscle > gills > heart > stomach > brain > haemolymph. Mr-GS expression and the glutamine concentrations were analyzed in the gills and muscle tissues of prawn under hyper/hypo-osmotic stress conditions. Under hyper-osmotic stress, the mRNA expression of Mr-GS was significantly increased in both gills and muscle at 3, 6 and 12 h post-treatment with 2.54, 4.21 and 10.83 folds, and 11.66, 17.97 and 45.92 folds, respectively. Protein analysis by western blot (WB) and Immunohistochemistry (IHC) further confirmed the Mr-GS expression was increased at 12 h post treatment. On the other hand, under hypo-osmotic stress, the mRNA expression of Mr-GS was also significantly increased in both gills and muscle at 3, 6 and 12 h post treatment with 1.63, 3.30 and 3.52 folds, and 4.06, 42.99 and 26.69 folds, respectively. Furthermore, under hyperosmotic stress, Gln concentration was increased in both gills and muscle at 6 and 12 h post treatment with 1.83, 2.02 folds, and 1.41, 1.29 folds, respectively. While, under hypo-osmotic stress, Gln concentration was increased in both gills and muscle at 3, 6 and 12 h post treatment with 3.99, 3.40, 2.59 folds, and 1.72, 1.83, 1.80 folds, respectively. Taken together, these results suggest that Mr-GS might play a key role in osmoregulation in M. rosenbergii.

physiology↗