De novo assembly and characterisation of chloroplast genomes of broccoli cvs. Marathon and Green sprout using next generation sequencing

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dc.authorid0000-0002-9577-9584en_US
dc.authorid0000-0003-3282-6272en_US
dc.authorid0000-0001-9618-3857en_US
dc.authorid0000-0001-6262-2866en_US
dc.contributor.authorZia, Ayisha
dc.contributor.authorAbdullah, Misbah Zahoor
dc.contributor.authorNisar, Asma
dc.contributor.authorBatool, Neelam
dc.contributor.authorBibi, Amana
dc.contributor.authorGürel, Ekrem
dc.date.accessioned2023-08-07T06:13:14Z
dc.date.available2023-08-07T06:13:14Z
dc.date.issued2022en_US
dc.departmentBAİBÜ, Fen Edebiyat Fakültesi, Biyoloji Bölümüen_US
dc.descriptionThis research work was funded by Higher Education Commission (HEC), Pakistan, under grant number: 7407/Federal/NRPU/R&D/HEC/2017. The authors acknowledge Mr. Irshad Khan for his technical support during the project.en_US
dc.description.abstractThe genus Brassica (family Brassicaceae) includes nutritionally and economically important species such as Brassica napus, Brassica rapa, and Brassica oleracea. Many varieties of B. oleracea are available in various morphological forms including nutritive vegetables such as cauliflower (var. botrytis), Brussels sprouts (var. gemmifera), kales and collards (var. acephala), kohlrabi (var. gongylodes), cabbage (var. capitata), and broccoli (var. italica). Objective of the present study was to sequence chloroplast genomes of two cultivars of broccoli: Marathon and Green sprout. The sequencing was done by next generation sequencing. The analysis was performed using Velvet, Geneious, GeSeq, tRNAscan-SE, ARAGORN, OrganellarGenomeDRAW, IRscope and REPuter. The genomes of both cultivars showed highly similar quadripartite structure of 153,365 bp. The LSC (83,136 bp) and SSC (17,835 bp) regions were separated by a pair of IR (26,197 bp) region. In total, 114 unique genes were present in both species, including 80 protein-coding, 30 tRNA and 4 rRNA genes, while 18 genes were duplicated in IRs. The highest amino acid encoding frequency was found for Leucine whereas cysteine was the least encoding amino acid. The codon usage analyses confirmed high encoding efficacy of codons that ended at 3'-end with A/T. Repeat analyses of these genomes revealed 415 microsatellites and 36 oligonucleotide repeats. Microsatellites motifs were mostly comprised of A/T instead of C/G. The comparative analyses confirmed the presence of 17 substitutions between both cultivars. Overall, this study will increase knowledge about the chloroplast genomes of broccoli and will provide a resource for chloroplast genetic engineering of this important edible plant.en_US
dc.description.sponsorshipHigher Education Commission (HEC), Pakistan [7407/Federal/NRPU/RD/HEC/2017]en_US
dc.identifier.citationZia, A., Zahoor, M., Abdullah, A., Nisar, A., Batool, N., Bibi, A., ... & Waheed, M. T. (2022). De novo assembly and characterisation of chloroplast genomes of broccoli cvs. Marathon and Green sprout using next generation sequencing. Turkish Journal of Agriculture and Forestry, 46(4), 525-535.en_US
dc.identifier.doi10.55730/1300-011X.3023
dc.identifier.endpage535en_US
dc.identifier.issn1300-011X
dc.identifier.issn1303-6173
dc.identifier.issue4en_US
dc.identifier.scopus2-s2.0-85136336780en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage525en_US
dc.identifier.trdizinid1141280en_US
dc.identifier.urihttp://dx.doi.org/10.55730/1300-011X.3023
dc.identifier.urihttps://hdl.handle.net/20.500.12491/11438
dc.identifier.volume46en_US
dc.identifier.wosWOS:000853383600009en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakTR-Dizinen_US
dc.institutionauthorGürel, Ekrem
dc.language.isoenen_US
dc.publisherScientific and Technological Research Council Turkeyen_US
dc.relation.ispartofTurkish Journal of Agriculture and Forestryen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectBroccolien_US
dc.subjectNext Generation Sequencingen_US
dc.subjectChloroplast Genomeen_US
dc.subjectOligonucleotide Repeatsen_US
dc.subjectSimple Sequence Repeatsen_US
dc.subjectCodon Usageen_US
dc.titleDe novo assembly and characterisation of chloroplast genomes of broccoli cvs. Marathon and Green sprout using next generation sequencingen_US
dc.typeArticleen_US

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