BACKGROUND: Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS: The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION: The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.

Department of Agronomy The University of Haripur Khyber Pakhtunkhwa Haripur 22620 Pakistan

Department of Botany The Islamia University Bahawalpur Pakistan

Department of Geology and Pedology Faculty of Forestry and Wood Technology Mendel University in Brno Zemedelska1 61300 Brno Czech Republic

Department of Pediatrics College of Medicine and King Khalid University Hospital King Saud University Medical City PO Box 2925 Riyadh 11461 Saudi Arabia

Department of Soil Science Faculty of Agricultural Sciences and Technology Bahauddin Zakariya University Multan 60800 Punjab Pakistan

Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource College of Tropical Crops Hainan University Haikou 570228 China

Jamil ur Rahman Center for Genome Research Dr Panjwani Center for Molecular Medicine and Drug Research International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan

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