Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in...Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants. The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons （ENC） for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon usage. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.展开更多
High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were ...High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment(including intron) of extremely GC-rich at the 5’ or/and 3’ flanking regions of these protein genes or their gene promoters.This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super "chromatin opening element" and plays an important role in mammalian gene expression.This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure,namely DNA GC-content.展开更多
基金supported in part by the Hi-Tech Re-search and Development Program of China ("863" Program) (No. 2007AA02Z329)the National Natural Science Foundation of China (Grant No. 20060213024)
文摘Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants. The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons （ENC） for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon usage. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.
文摘High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment(including intron) of extremely GC-rich at the 5’ or/and 3’ flanking regions of these protein genes or their gene promoters.This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super "chromatin opening element" and plays an important role in mammalian gene expression.This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure,namely DNA GC-content.
文摘采用PCR直接测序法对伞形科（ Apiaceae）前胡族（ Trib. Peucedaneae）种类川明参（ Chuanminshen violaceum Sheh et Shan）、泰山前胡〔Peucedanum wawrae （ H. Wolff） Su〕和华中前胡（ P. medicum Dunn）以及美味芹族（ Trib. Smyrnieae）种类明党参（Changium smyrnioides H. Wolff）、宝兴棱子芹（Pleurospermum davidii Franch.）、丽江棱子芹（ P. foetens Franch.）和鸡冠棱子芹（ P. cristatum de Boiss.）的叶绿体基因组psbA-trnH片段进行了扩增测序,获得的序列已提交至GenBank,登录号为KF557756-KF557762。结合引自GenBank的前胡族阿魏属（ Ferula Linn.）1种、大瓣芹属（ Semenovia Regel et Herder）1种、当归属（ Angelica Linn.）2种和美味芹族的舟瓣芹属（ Sinolimprichtia H. Wolff）1种、羌活属（ Notopterygium de Boiss.）1种、瘤果芹属（ Trachydium Lindl.）1种以及针果芹族（ Trib. Scandicineae）刺果芹〔Turgenia latifolia （ Linn.） Hoffm.〕的psbA-trnH片段序列,对各种类的psbA-trnH片段信息进行分析；并以刺果芹为外类群构建了MP、ML和BI系统发育树。结果表明：川明参和明党参的psbA-trnH片段长度均为258 bp、GC含量均为23％,而其他种类的psbA-trnH片段长度为228~405 bp、GC含量为26％~35％；排序后psbA-trnH 序列总长度为553 bp（包括空位）,其中变异位点237个、信息位点178个。川明参与明党参间的相对遗传距离最小（仅为0.02）,而川明参与其他种类间的相对遗传距离为0.10~1.34,且总体上川明参与美味芹族种类的相对遗传距离较小,表明川明参与明党参及美味芹族种类的亲缘关系较近。在3类系统树上,川明参与明党参均聚在一起,并与美味芹族的属种聚为一大支,而远离由前胡族属种构成的另一大支。结合外部形态和果实解剖结构特征,建议将川明参属（ Chuanminshen Sheh et Shan ）从前胡族中分出并置于美味芹族中,与明党参属（ Changium H. Wolff）为姐妹类群�
