Biology subjects

Thimma, M.

Publications and source records attributed to Thimma, M..

4 recordsLinked to original sources

bioRxiv2024

Oryza genome evolution through a tetraploid lens

Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) and 25 diploid and tetraploid wild species, 11 extant genome types, and a [~]3.4-fold genome size variation - that possesses a virtually untapped reservoir of genes that can be used for crop improvement. Here we unveil and interrogate 11 new chromosome-level assemblies of nine tetraploid and two diploid wild Oryza species in the context of [~]15 million years of evolution of the genus. We show that the core Oryza (sub)genome across all genome types is only [~]200 Mb and largely syntenic, while the remaining nuclear fractions, spanning [~]80-600 Mb, are intermingled, extremely plastic and rapidly evolving. For the halophyte O. coarctata, we show that - despite the detection of gene fractionation in the subgenomes - homoeologous genes are expressed at higher levels in one subgenome over the other in a mosaic form, thereby showing subgenome equivalence. The integration of these 11 new ultra-high quality reference genomes with our previously published genome data sets provide a nearly complete picture of the consequences of natural and artificial selection across the evolutionary history of Oryza. This in turn opens the door to unlock their genetic potential for future crop improvement and neodomestication.

genomics↗

bioRxiv2023

HPC-based genome variant calling workflow (HPC-GVCW)

A high-performance computing genome variant calling workflow was designed to run GATK on HPC platforms. This workflow efficiently called an average of 27.3 M, 32.6 M, 168.9 M, and 16.2 M SNPs for rice, sorghum, maize, and soybean, respectively, on the most recently released high-quality reference sequences. Analysis of a rice pan-genome reference panel revealed 2.1 M novel SNPs that have yet to be publicly released.

genomics↗

bioRxiv2022

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice (O. sativa), plus the genomes of two close relatives (O. rufipogon and O. punctata), we built a pan-genome inversion index of 1,054 non-redundant inversions that span an average of [~] 14% of the O. sativa cv. Nipponbare reference genome sequence. Using this index we estimated an inversion rate of 1,100 inversions per million years in Asian rice, which is 37 to 73 times higher than previously estimated for plants. Detailed analyses of these inversions showed evidence of their effects on gene regulation, recombination rate, linkage disequilibrium and agronomic trait performance. Our study uncovers the prevalence and scale of large inversions ([≥] 100 kb) across the pan-genome of Asian rice, and hints at their largely unexplored role in functional biology and crop performance.

genomics↗

bioRxiv2019

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

Aside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.

genomics↗