K, S. K. | bioRxiv Science

bioRxiv2026

Genome Assembly of the Iconic Samba Mahsuri Delineates Locus-specific Population Structure within Indica Rice

High-quality reference genomes enable detailed analysis of structural variation and its consequences for genome organization in crops. Here, we present a chromosome-scale genome assembly of Oryza sativa cv. Samba Mahsuri (SM), an elite Indian mega rice variety cultivated for its grain and cooking quality. Using PacBio HiFi sequencing in combination with Illumina reads and Bionano optical mapping, we generated a [~]395 Mb assembly (SMv1.0) with 97.7% BUSCO completeness. A robust annotation framework identified 31,138 evidence-guided protein-coding gene models alongside 59,152 ab initio predictions. Comparative genomic analyses revealed extensive macrosynteny with established rice reference genomes, while uncovering pronounced locus-specific sequence and structural polymorphisms. Notably, a complex inversion-match-inversion (IMI) configuration on chromosome 6 differentiates SM from the japonica reference Nipponbare, but not from the indica reference R498. Population-scale analyses of 533 cultivated and 4 wild rice accessions demonstrate that genetic variation within the IMI region produces a markedly sharper and more coherent population structure than is observed in flanking regions or genome-wide, including tight subpopulation-based clustering and segregation of alternative IMI configurations within indica rice. Together, these results establish SMv1.0 as a robust chromosome-scale reference genome sequence for rice and demonstrate how large structural polymorphisms can shape locus-specific patterns of relatedness that diverge from genome-wide ancestry. Significance StatementWe present a high-quality chromosome-scale genome sequence of the elite Indian rice variety Samba Mahsuri (SM), which, to the best of our knowledge, represents the first chromosome-scale reference genome from Indian rice germplasm assembled using a map-based method. Using this reference to analyze population-scale genotyping data from 533 cultivated and four wild rice accessions reveals markedly tighter population clustering within a megabase-scale inversion (IMI) region, than at the whole-genome scale, along with a pronounced split within indica rice that is independent of genome-wide ancestry.

plant biology↗

bioRxiv2023

Oxidative stress biomarkers in hypothyroid, non thyroid illness and euthyroid dogs

There are only a few numbers of published reports available on oxidative stress parameters in hypothyroidism and many of which are in the field of human medicine. Studies on hypothyroidism in dogs lack an assessment of oxidative stress and some are vague and inconclusive. So, the current study was formulated primarily to address variations in chief antioxidant parameters in dogs with hypothyroidism, non-thyroid illness and euthyroidism. Secondly, magnitude of oxidative stress was measured in hypothyroid dogs prior to and during the course of levothyroxine therapy, which were compared statistically. Evaluation of thyroid profile (TT4, fT4 and cTSH) was carried out prior to the assessment of oxidative stress biomarkers such as, serum malondialdehyde (MDA), superoxide dismutase (SOD), reduced glutathione (GSH) and catalase. A total of 45 dogs were employed in the study, that includes 19 dogs with hypothyroidism, 11 dogs with non-thyroid illness and 15 dogs with euthyroidism. These dogs were brought either to the dermatological unit or the immunization unit. Dogs were divided into three groups: group 1 represented hypothyroidism (low fT4 or low TT4 and high cTSH); group 2 represented non-thyroid disease (low or normal TT4 and low cTSH i.e., inconclusive levels of thyroid hormones); and group 3 represented dogs with normal thyroid levels (euthyroid dogs). Descriptive statistics and normality plots were carried out using SPSS software version 21. Assuming that the variances were unequal, P values were calculated and compared by one-way ANOVA, post hoc multiple comparison analysis using the Games-Howell test. The mean thyroid hormone levels of hypothyroid dogs before (Day 0) and after (Day 60) treatment was significantly different (P<0.05). Hypothyroid dogs (group 1) displayed significantly lower mean fT4 levels (0.56{+/-}0.07) and higher mean cTSH levels (8.14{+/-}1.17) when compared to other groups. The mean values of serum biochemical parameters showed significant differences among groups (P<0.01). Various biomarkers showed a significant alteration viz., there was a significant reduction in catalase, SOD, GSH and increase in MDA in hypothyroid dogs when compared with euthyroid dogs. However, following therapy for 60 days, catalase, SOD and GSH levels elevated and MDA level reduced significantly and reached nearly to that of euthyroid dogs. Further, there was no significant difference between NTI and euthyroid dogs which demonstrated the antioxidant defence against oxidative stress in hypothyroid dogs. As an outcome, antioxidant measures and serum biochemical tests can be employed as a diagnostic tool to rule out oxidative stress in hypothyroid dogs.

physiology↗