Complete structure of the chloroplast genome of Arabidopsis thaliana.

The complete nucleotide sequence of the chloroplast genome of Arabidopsis thaliana has been determined. The genome as a circular DNA composed of 154,478 bp containing a pair of inverted repeats of 26,264 bp, which are separated by small and large single copy regions of 17,780 bp and 84,170 bp, respectively. A total of 87 potential protein-coding genes including 8 genes duplicated in the inverted repeat regions, 4 ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acid species were assigned to the genome on the basis of similarity to the chloroplast genes previously reported for other species. The translated amino acid sequences from respective potential protein-coding genes showed 63.9% to 100% sequence similarity to those of the corresponding genes in the chloroplast genome of Nicotiana tabacum, indicating the occurrence of significant diversity in the chloroplast genes between two dicot plants. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.     

Nodule Organogenesis in Lotus japonicus

Lotus japonicus. Received 25 September 2000/ Accepted in revised form 9 October 2000     

藻类植物叶绿体基因组研究进展

藻类植物的cpDNA结构复杂,普遍缺失反向重复序列IR,且存在IR的藻类植物种类的cpDNA也有IR变短退化迹象.藻类植物的cpDNA包含的基因一般比高等植物要多,编码能力更强.藻类植物cpDNA全序列的测定方法主要是Fosmid文库构建,配合使用Long-PCR技术.该文对国内外有关藻类植物叶绿体基因组结构、叶绿体编码基因、叶绿体基因组在藻类系统发育中的应用以及藻类植物叶绿体基因组的提取和序列测定方法等进行综述,为藻类植物的系统发育和叶绿体起源以及功能基因组学的研究提供理论依据.     

Plastid genome sequencing,comparative genomics,and phylogenomics:Current status and prospects

More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies.Based on this unprecedented abundance of data,extensive genomic changes have been revealed in the plastid genomes.Inversion is the most common mechanism that leads to gene order changes.Several inversion events have been recognized as informative phylogenetic markers,such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putat...     

孑遗濒危植物矮扁桃叶绿体全基因组特征分析及亲缘关系鉴定

对第三纪孑遗濒危植物矮扁桃（Amygdalus nana）叶绿体全基因组进行结构特征分析,并探究其与近缘物种之间的系统进化关系。利用Illumina HiSeq Xten测序技术获取叶绿体全基因组序列,对其进行组装、注释和特征分析。结果表明：①矮扁桃叶绿体全基因组总长度为158 596 bp,其中LSC长度为86 771 bp,SSC长度为19 037 bp,2个IRs均为26 394 bp,为环状四分体结构。共注释130个基因,包括85个PCGs、37个tRNA和8个rRNA。②对6种植物进行IR边界区扩张和收缩分析,发现在4个边界区的基因类型和基因分布情况存在一定差异,并且亲缘关系越紧密差异程度越小。③在矮扁桃叶绿体全基因组中共预测了71个SSRs位点。④系统发育分析结果显示,在扁桃亚属中,矮扁桃在亲缘关系上与蒙古扁桃更近,而与长柄扁桃和榆叶梅的亲缘关系稍远。本研究对矮扁桃叶绿体全基因组进行了深度剖析,并且涉及大量被子植物的叶绿体全基因组资料,为桃属植物之间的进化关系和植物鉴定提供参考依据。     

西北干旱区孑遗濒危植物四合木(Tetraena mongolica)叶绿体基因组特征研究及比较分析

四合木（Tetraena mongolica）是我国特有的蒺藜科（Zygophyllaceae）强旱生小灌木;因其起源古老、抗逆性强;所以可作为生物多样性起源和环境演变研究的理想对象;具有重要的学术研究价值。本研究采用Illumina双末端测序技术对四合木叶绿体基因组进行建库测序和分析。选取蒺藜目及牻牛儿苗目共计30个物种叶绿体基因组;与四合木进行系统发育关系分析探讨。结果表明:四合木叶绿体基因组长度为106 259 bp;其中反向重复区（IR区中）有7种基因;包括4种PCG基因;3种tRNA基因。叶绿体基因组共编码98种基因;包括65种蛋白编码基因、29种tRNA基因与4种rRNA基因。生物信息学表明;在四合木中共搜到92个SSR位点;其中包括74个单核苷酸重复基序;7个二核苷酸重复基序;1个三核苷酸重复基序;9个四核苷酸重复基序和1个五核苷酸基序。没有发现六核苷酸;其中单核苷酸重复在四合木的叶绿体基因组SSR中占比为80.1%。通过MEGA软件采用近邻结合法（neighbor-joining;NJ）对四合木等31个物种的叶绿体基因组进行聚类分析;发现四合木与蒺藜科三齿拉雷亚灌木为最近的姐妹种;其次为牻牛儿苗科智利白桦植物亲缘关系较近;与牻牛儿苗科天竺葵属和牻牛儿苗科高桂花属亲缘关系最远;说明四合木属于蒺藜科物种;这对于四合木的研究等具有一定的参考价值。     

植物基因工程新途径：叶绿体转化

在植物基因工程研究中,叶绿体是继核转化之后又一新的遗传转化和表达受体,叶绿体转化体系具有可同时进行多基因转化,表达原核性,超量表达,后代遗传稳定,定点整合,不会产生基因沉默及母性遗传和安全性好等特点,本文着重介绍叶绿体转化体系的特点,国内外研究动态,存在的问题及未来发展方向。     

长柄扁桃叶绿体基因组比较

蔷薇科桃属植物长柄扁桃Amygdalus pedunculata Pall.是我国重点发展的12种木本油料作物之一.将自然生长在陕西省榆林市毛乌素沙地的长柄扁桃进行高通量测序、组装得到了GenBank登录号为MG602257的长柄扁桃叶绿体基因组.与NCBI中其他两个长柄扁桃叶绿体基因组(MG869261和KY1011...     

衣藻叶绿体遗传转化的研究

叶绿体遗传转人是近几年发展起来的新领域。本文主要介绍了叶绿体遗传转化的特点、基本原理和衣藻叶绿体遗传转化的方法与技术;     

鲁桑叶绿体基因组序列及特征分析

鲁桑(Morus multicaulis)是亚洲地区栽培的重要经济作物。以鲁桑品种日本胡橙为实验材料, 利用高通量测序技术对鲁桑叶绿体基因组进行测序, 获得NCBI登录号(KU355297), 并研究鲁桑的叶绿体基因组结构。结合前人对蒙桑(M. mongolica)、印度桑(M. indica)和川桑(M. notabilis)的研究结果, 对鲁桑的系统进化关系进行了探讨。研究结果表明: 鲁桑叶绿体基因组是一个典型的四部分结构, 全长159 154 bp, 共注释130个基因, 包含85个蛋白质编码基因(18个基因在反向重复区重复)、37个转运RNA (tRNA)基因和8个核糖体RNA (rRNA)基因。生物信息学分析表明, 在鲁桑中共搜索到82个SSR位点, 单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序个数分别为63、7、2、9和1个, 并没有发现六核苷酸; 其中单核苷酸重复在鲁桑的叶绿体基因组SSR中占76.8%。采用MEGA 6.0软件, 通过最大似然法和近邻结合法对包括4个桑属物种在内的15个物种的叶绿体基因组序列进行聚类分析, 2种方法得到的聚类结果均为鲁桑和蒙桑聚在一起。研究结果对叶绿体基因组工程研究及桑属种间的分子标记开发和优良品种培育具有一定的参考价值。     

百脉根嫁接方法的优化及其在结瘤自调控研究中的应用

嫁接试验是研究结瘤自调控的有效方法。本文优化了百脉根的嫁接方法,并应用该方法初步研究了百脉根突变体rel3根瘤数目减少的机理。结果表明,rel3突变体根瘤数目减少的表型是由来自于茎的信号决定。     

航天诱变百脉根结瘤突变体的筛选

通过返回式卫星搭载,利用太空环境对百脉根(Lotus japonicus)MG-20种子进行诱变。从种植的三代植株中,筛选到多种共生固氮根瘤的突变体,其中不结根瘤突变体18个株系,表现为接种根瘤菌两周后无根瘤形成;结无效根瘤突变体9个株系,表现为根瘤数目少且分布不均匀,根瘤呈白色,有些为半透明;花叶形态异常突变体1个株系,表现为除根瘤数目少外,植株矮小、托叶消失、花形态异常;纤细突变体1个株系,表现为除根瘤数目少外,植株变小、茎细叶小。     

百脉根LjCYC1基因克隆及其蛋白核定位

通过筛选百脉根(Lotus 7aponicus)基因组文库,克隆了LjCYC1(Lotus japonicus Cycloidea-like1)基因.L7CYC1是金鱼草(Antirrhium)CYC (Cycloidea)基因的同源基因,CYC属于TCP[TBl(teosinte branchedl),CYC,PCFs(PCFl and PCF2)]基因家族,编码转录调控子控制金鱼草花的对称性.基因组序列分析表明,LjCYC1的开放阅读框(ORF)由两个外显子和一个内含子组成,其cDNA编码的LjCYC1蛋白包含了370个氨基酸.蛋白序列分析显示,LjCYC1包含一个TCP结构域和一个R结构域,属于TCP结构域蛋白家族的CYC/TBl亚家族;LjCYCl氨基酸序列与CYC相比,一致性和相似性分别为39.0%和42.6%.不同长度的LjCYCl-cDNA与报告基因GUS融合后,通过粒子轰击(particle bombardment)方法在洋葱表皮细胞瞬时表达融合蛋白,观察到包含了TCP结构域的融合蛋白能够进行细胞核定位,提示LjCYCl可能作为转录因子行使功能;TCP结构域自身不能完成核定位过程,还需要结构域两侧旁邻氨基酸序列的协助.     

Generation of 7137 non-redundant expressed sequence tags from a legume, Lotus japonicus.

For comprehensive analysis of genes expressed in a model legume, Lotus japonicus, a total of 22,983 5' end expressed sequence tags (ESTs) were accumulated from normalized and size-selected cDNA libraries constructed from young (2 weeks old) plants. The EST sequences were clustered into 7137 non-redundant groups. Similarity search against public non-redundant protein database indicated that 3302 groups showed similarity to genes of known function, 1143 groups to hypothetical genes, and 2692 were novel sequences. Homologues of 5 nodule-specific genes which have been reported in other legume species were contained in the collected ESTs, suggesting that the EST source generated in this study will become a useful tool for identification of genes related to legume-specific biological processes. The sequence data of individual ESTs are available at the web site: http://www.kazusa.or.jp/en/plant/lotus/EST/.     

Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape

Connecting broad-scale patterns of genetic variation and population structure to genetic diversity on a landscape is a key step towards understanding historical processes of migration and adaptation. New genomic approaches can be used to increase the resolution of phylogeographic studies while reducing locus sampling effects and circumventing ascertainment bias. Here, we use a novel approach based on high-throughput sequencing to characterize genetic diversity in complete chloroplast genomes and >10,000 nuclear loci in switchgrass, at continental and landscape scales. Switchgrass is a North American tallgrass species, which is widely used in conservation and perennial biomass production, and shows strong ecotypic adaptation and population structure across the continental range. We sequenced 40.9 billion base pairs from 24 individuals from across the species' range and 20 individuals from the Indiana Dunes. Analysis of plastome sequence revealed 203 variable SNP sites that define eight haplogroups, which are differentiated by 4-127 SNPs and confirmed by patterns of indel variation. These include three deeply divergent haplogroups, which correspond to the previously described lowland-upland ecotypic split and a novel upland haplogroup split that dates to the mid-Pleistocene. Most of the plastome haplogroup diversity present in the northern switchgrass range, including in the Indiana Dunes, originated in the mid- or upper Pleistocene prior to the most recent postglacial recolonization. Furthermore, a recently colonized landscape feature (approximately 150 ya) in the Indiana Dunes contains several deeply divergent upland haplogroups. Nuclear markers also support a deep lowland-upland split, followed by limited gene flow, and show extensive gene flow in the local population of the Indiana Dunes.