Biology subjects

Mondal, T. K.

Publications and source records attributed to Mondal, T. K..

4 recordsLinked to original sources

bioRxiv2025

QTLIT: A user-friendly Shiny app for Quantitative Trait Loci (QTL) analysis

Identification of Quantitative Trait Loci from DNA sequence data is a multistep process, which is difficult for the plant breeders. To make the QTL identification breeders friendly, we developed QTLIT, a tool comprised of popular R packages and open sources software under a single umbrella for QTL analysis that enables intuitive exploration, multidimensional analyses, and visualization of results generated from any kind of DNA sequence data that deals with Single Nucleotide Polymorphism (SNP) variation. This tool requires raw or processed FASTQ files and proceed it for SNP identification to further perform QTL analysis on genomic regions of interest along with phenotyping data of various pedigree-based mapping populations. QTLIT generates a full range of plots such as VCF quality, linkage map, LOD score etc. It has broad range of applications and options for different parameters which the user can adjust as per their requirements. Moreover, it has two separate interfaces where one can utilize this tool to generate alignment files and/or variant calling for other downstream analysis. QTLIT is a fast and intuitive QTL analysis tool suitable for a wide range of users due to its architecture and its user-friendly graphical interface. QTLIT source code is available at https://github.com/TKM-Lab/QTLIT and the user interface version is available on http://14.139.229.202:8080/QTLIT.

genomics↗

bioRxiv2020

C4 photosynthesis with Kranz anatomy evolved in the Oryza coarctata Roxb.

The C4 cycle is a complex biochemical pathway that has been evolved in plants to deal with the adverse environmental conditions. Mostly C4 plants grow in arid, water-logged area or poor nutrient habitats. Wild species, Oryza coarctata (genome type KKLL; chromosome number (4x) =48, genome size 665 Mb) belongs to the genus of Oryza which thrives well under high saline as well as submerged conditions. Here, we report for the first time that O. coarctata is a C4 plant by observing the increased biomass growth, morphological features such as vein density, anatomical features including ultrastuctural characteristics as well as expression patterns of C4 related genes. Leaves of O. coarctata have higher vein density and possess Kranz anatomy. The ultrastructural observation showed chloroplast dimorphism i.e. presence of agranal chloroplasts in bundle sheath cells whereas, mesophyll cells contain granal chloroplasts. The cell walls of bundle sheath cells contain tangential suberin lamella. The transcript level of C4 specific genes such as phosphoenolpyruvate carboxylase, pyruvate orthophosphate dikinase, NADP-dependent malic enzyme and malate dehydrogenase was higher in leaves of O. coarctata compare to high yielding rice cultivar (IR-29). These anatomical, ultra structural as well as molecular changes in O. coarctata for C4 photosynthesis adaptation might be might be due to its survival in wide diverse condition from aquatic to saline submerged condition. Being in the genus of Oryza, this plant could be potential donor for production of C4 rice in future through conventional breeding, as successful cross with rice has already been reported.

plant biology↗

bioRxiv2020

Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

Tea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

genomics↗

bioRxiv2019

Draft genome sequence of a popular Indian tea genotype TV-1

Camellia assamica L. (O). Kuntze. var. TV-1 from Assam, India is one of the most important tea cultivar of Indian Tea Industry which botanically belongs to Assam type and has distinct morphological as well as chemical constituent in leaf than China type of tea. We here present the first draft genome sequence of TV-1, assembled in 2.93 Gb size comprising of 14,824 scaffolds and covering 97.66% of the predicted genome size (3.0 Gb) as determined by flow cytometry. The N50 value, longest and average contig size for this draft genome was found to be as 538.96 Kb, 3.64 Mb and 197.99 Kb, respectively. There were 495,747 SSRs (Di- to Hexa-mers) in the genome and the repeat contents accounted for 71.87% of the genome. About 94.40% genome completeness was predicted with BUSCO, maximum among the published and reported tea genomes. The clustering of the assembled genome with Hi-C data resulted in 15 clusters ranging from the size of 631.46 Mb to 14.39 Mb and accounting 99.32% of assembled genome. This data will act as the starting point for unravelling the important genes and differentiating Indian tea from other commercially available tea varieties.

plant biology↗