Genome Assembly for Draft Genome Sequence of Sphingobium lucknowense strain F2T Isolated from an HCH Dumpsite in Ummari Village,Lucknow,India.
-By Shreyasi Das,
Department of Zoology,
University of Delhi.
Since the dawn of intelligence science has been striding forward with innovations from every corner of the world.
Biology has been making advent at a slightly greater pace,out of the laboratory and into silicon chips,Since days bygone, study of living beings required to break barriers of the single cell and throw light into hereditary material,giving us great insights into nucleic acid sequences.To face the challenges associated with various questions thrown at biology,great advent required being made in the field of working out the correct order of how nucleic acids are arranged in an array of genes to give rise to various phenotypes and often, its deviations. Thus, arose the requirement of sequencing the hereditary material,knowing about the entire genetic content of the organism or rather,it’s genome and its analysis.
With the help of sequencing a great number of laboratories across the globe have conducted groundbreaking research and this very important technique has been established as the basis of a plethora of investigations
REASON BEHIND CHOOSING GENOME ASSEMBLY:
From research laboratories to personalized genome analysis,genome sequencing and downstream processing of the sequenced data has become a mandate for most biological experimentation.
Here,we look into genome sequencing,assembly and annotation in general and apply them on our organism of interest Sphingobium lucknowense Strain F2T .S. lucknowense is a hexachlorocycleohexane(HCH) degrading bacterium that was isolated from HCH contaminated soil in Ummari village,Lucknow, India.(Garg N. et. Al.,2012)
Why a bacterium?
The answer to this question lies in the fact that bacteria are easier to study than eukaryotes.
They are unicellular,so all life processes can be studied within a single cell.
Having a cell wall renders them resistant to osmolysis or contamination and several toxic chemicals.
They often bear many innate or acquired genes,rendering them chemical resistance. Due to the lack of a nuclear membrane and histone packaging,these are easy targets for gene manipulation experiments.
Small size makes them easier to handle and ease of culture is another advantage with bacteria.
We use a Sphingobium due to:
Bacteria from the genus Sphingobium have the capability to degrade several organic compounds like toluene,phenol,homogentisate,etc. Above all,it has the capability to degrade HCH which was previously known as BHC(Benzene Hexachloride).
HCH is a cyclic, saturated, chlorinated hydrocarbon that has been used extensively for the control of agricultural pests and in health programmes since the 1950s. Two forms of HCH have been used: technical HCH [a mixture of four HCH isomers: α (60 -70 %), β (5–12 %),...