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CHLOROPLAST GENOME SEQUENCING OF AJUGA BRACTEOSA AND ITS PHYLOGENETIC RELATIONSHIP IN FAMILYLAMIACEAE

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Author: NOSHEELA RIAZ

Citable URI : https://vspace.vu.edu.pk/detail.aspx?id=370

Publisher : Virtual University

Date Issued: 7/6/2020 12:00:00 AM

Abstract

Medicinal plants were playing an important role in our lives due to their remedial properties. Lifesaving medicines were produced by these plants. For their better use in food and medicines genomes sequencing of these medicinal plants was needed. Ajuga bracteosa is a medicinal plant in family Lamiaceae (mint family). It is a herbal plant and used in many medicines. In this research work chloroplast genome sequencing of Ajuga bracteosa was carried out by next generation sequencing technique. DNeasy plant DNA extraction kit was used for the extraction of DNA from fresh young leaves of Ajuga bracteosa. Quality and quantity of DNA was evaluated using agarose gel electrophoresis and uDrop plate of Multiskan GO spectrophotometer. DNA was lyophilized before shipment to Novagene, Hong Kong, a commercial NGS facility. Sequencing was done using Illumina HiSeq 2500 instrument, using PE150 run, and approx. 4Gb data was produced. Quality of short reads was checked using SolexaQA tool. Short reads were mapped back to Ajuga reptans chloroplast genome downloaded from NCBI. Mapping was visualized using Tablet tool, which attested to high coverage depth of chloroplast genome. The genome was de novo assembled using Velvet tool, and several velvet runs were performed by changing kmer values. Assembled contigs from these Velvet runs were imported in Geneious tool and used to generate full length chloroplast genome. The assembled genome size was 150,373 bp, divided in usual LSC, SSC and IRs. Overall genome structure and gene synteny matched to Ajuga reptans chloroplast genome. Phylogenetic analysis showed divergence of Ajuga bracteosa from its relatives in family Lamiaceae. This study showed intra specific and interspecific relationship within family Lamiaceae. So, this work will help the researchers in proper identification and differentiation of Ajuga bracteosa from the other plants of same family.


URI : https://vspace.vu.edu.pk/details.aspx?id=370

Citation: RIAZ,N(2019),CHLOROPLAST GENOME SEQUENCING OF AJUGA BRACTEOSA AND ITS PHYLOGENETIC RELATIONSHIP IN FAMILYLAMIACEAE,VIRTUAL UNIVERSITY OF PAKISTAN.(Lahore,Pakistan).

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