Ambardar, S. | bioRxiv Science

bioRxiv2021

De-novo draft genome sequence of Crocus Sativus L, Saffron, a golden condiment.

Crocus sativus L, saffron is the highest priced but low yielding plant of medicinal and culinary importance. Despite its economic status, the omic information on this plant is very scarce, with only a couple of transcriptomics and epigenetic studies. In the present study, the draft genome sequence of C. sativus has been assembled using Illumina sequencing. In fact, this is the first genome sequence from any member of family Iridaceae. Genome size of C. sativus was estimated to be 3.5 Gb and the draft genome is 3.01 Gb long with 84.24% genome coverage. In total, 8,62,275 repeats and 9,64,231 SSR markers have been identified. A total of 53,546 functional genes were annotated, out of which, 43,649 proteins were associated with GO annotation. 5726 proteins were identified as transcription factors, with MYB & MYB related family proteins being more abundant. Orthology analysis of C. sativus with 3 different monocot species of the same plant order and rice (model monocot plant) revealed 7328 proteins clusters to be conserved in all the five plant species, whereas 2510 proteins cluster were unique to C. sativus only. 10,912 unigenes of C. sativus were mapped to 387 KEGG pathways of monocot. The genes involved in the pathway of apocarotenoids biosynthesis (crocin, crocetin, picrocrocin, and safranal) were present in the draft genome.

genomics↗

bioRxiv2019

Studying cellular functions in bipolar disorder: Are there specific predictors of lithium response?

BackgroundLithium is the first-line mood stabilizer for the treatment of bipolar disorder (BD). In order to interrogate cellular phenotypes related to disease and lithium treatment response, this study used neural precursor cells (NPCs) and lymphoblastoid cell lines (LCLs) from BD patients who are well characterized for clinical lithium response.\n\nMethodsBD patients diagnosed according to the DSM-IV criteria; were recruited from the outpatient services of the National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India. Clinical lithium response was assessed using the \"Alda scale\" and \"NIMH Retrospective Life chart method\". The controls were ethnically matched healthy subjects with no family history of neuropsychiatric illness. NPCs from two BD patients from the same family who clearly differed in their clinical response to lithium were chosen, and compared with healthy population controls. Whole transcriptome sequencing (RNA-Seq) and analysis were performed, with and without in vitro lithium (1mM for 7 days). In addition, mitochondrial membrane potential (MMP), cell viability and cell proliferation parameters were examined. Experiments were also performed in 25 LCLs from BD patients (16 lithium responders and 9 lithium non-responders), and 12 healthy control LCLs, to evaluate them in a system amenable to clinical translation.\n\nResultsRNA-Sequencing and analysis did not reveal differences in NPCs on in vitro lithium treatment. MMP was lower in BD, both in NPCs and LCLs; reversal with in vitro lithium happened only in LCLs and was unrelated to lithium response. Cell proliferation was higher in BD compared to controls, and there was no change on lithium addition. Cell viability assays indicated greater cell death in BD; which could only be rescued in LCLs of clinical lithium responders. The latter finding was associated with enhanced BCL2 and GSK3B expression with in vitro lithium.\n\nDiscussionOverall, our study findings indicate that there are cellular phenotypes related to the disease (mitochondrial potential, cell proliferation) in NPCs and LCLs. We also observed clinical lithium response related phenotypes (cell viability, BCL2/ GSK3B expression) in LCLs. The next step would be to evaluate a larger set of PBMCs from clinical lithium response groups of BD to derive cellular phenotypes related to direct clinical application.

neuroscience↗