背景:FarsetiahamiltoniiRoyle是一种来自Cholistan沙漠的重要药用一年生植物,属于十字花科的Anastaticeae和进化枝C。我们提供了哈密顿氏杆菌完整的叶绿体序列,使用IlluminaHiSeq2500和配对末端测序获得。我们比较了F.Hamiltonii和其他9种C进化枝,包括Farsetiaoccidentalis,Lobularialibyca,Notocerasbicorne,Paroliniaornata,Morettiacanescens,Cochleariaborzaeana,巨无霸,Biscutellalaevigata,还有IberisAmara.我们对22种十字花科进行了系统发育研究,其中包括来自17个部落和6个分支的成员。
结果:哈密顿氏杆菌的叶绿体基因组序列大小为154,802bp,GC含量为36.30%,具有由83,906bp的大型单拷贝(LSC)组成的典型结构,一个17,988bp的小拷贝(SSC),和两个26,454bp的反向重复序列(IRs)拷贝。哈密顿F.和西花F.的基因组显示出共有的氨基酸频率和密码子使用,RNA编辑位点,简单的序列重复,和寡核苷酸重复。最大似然树揭示了Farsetia是单系属,和莫雷蒂亚有密切联系,引导得分为100。颠换取代率(Tv)高于过渡取代率(Ts),在与F.Hamiltonii的所有比较中,导致Ts/Tv小于1,表明这些物种密切相关。在所有与哈密顿氏杆菌的比较中,同义替换(Ks)的比率都大于非同义替换(Ka)。当Ka/Ks比值小于1时,表明基因经历了纯化选择。低核苷酸多样性值范围从0.00085到0.08516,IR区域包含连接上的相当基因,变化最小,支持十字花科C进化枝的选定叶绿体基因组的保守状态。我们确定了十个多态性区域,包括rps8-rpl14,rps15-ycf1,ndhG-ndhI,psbK-psbI,ccsA-ndhD,rpl36-rps8,peta-psbJ,ndhF-rpl32,psaJ-rpl3和ycf1,可用于构建真正且廉价的方法,以解决分类学差异并了解十字花科物种之间的系统发育关系。
结论:哈密顿氏杆菌的整个叶绿体测序揭示了进化枝C的成员之间的叶绿体序列的差异。完整的F.hamiltonii叶绿体将用作对该属进行全面分类学研究的来源。哈密顿氏杆菌和其他进化枝C物种的比较为进化枝的系统发育数据和进化过程增加了新的信息。这项研究的结果还将提供进化枝C叶绿体的进一步分子用途,用于可能的植物遗传修饰,并将有助于识别更多的十字花科物种。
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.
CONCLUSIONS: 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.