裂叶榆叶绿体基因组及CP-SSR位点分析

榆树材质优良,具有良好的耐旱、耐寒和耐盐碱能力,从温带、暖温带到亚热带都有分布。本研究对榆科植物(裂叶榆)的叶绿体基因组进行De novo测序,裂叶榆叶绿体基因组序列全长为158953 bp,为典型的四段式结构,其中LSC区长度为88032 bp,SSC区长18846 bp,两个IR区长26037 bp,GC含量为35. 57%。裂叶榆叶绿体基因组总共编码139个基因,包括85个蛋白编码基因、8个r RNA和46个t RNA基因。裂叶榆的叶绿体基因组存在755个SSR位点,SSR序列长度主要以6~8 bp的短序列为主,SSR共有49个重复单元,以A/T和AT/AT为主,占所有SSR位点的66. 09%。选取42个物种叶绿体基因组的共有蛋白编码基因进行系统进化分析表明,裂叶榆与大麻科、桑科物种亲缘关系最近,榆科与大麻科、桑科均属于荨麻目,与传统分类学相吻合。本研究报道了裂叶榆的叶绿体基因组序列,对今后榆树的光合作用研究、CP-SSR引物开发、进化研究及叶绿体转基因工程等研究具有重要意义。     

金莲花叶绿体基因组测序及特征分析

金莲花(Trollius chinensis)是毛茛科的一种药用及观赏植物,采用Illumina HiSeq2500高通量技术对其全基因组DNA测序,建立126 bp DNA小片段文库,以大兔葵(Megaleranthis saniculifolia)叶绿体基因组为参考,通过BLASTN比对提取后用CLC Genomics Workbench软件组装得到金莲花叶绿体全基因组序列,并对其特征进行分析。结果表明,金莲花叶绿体基因组全长160 191 bp,具有典型的被子植物叶绿体基因组环状四分体结构,两个反向互补重复序列(inverted repeat, IRA和IRB)的长度均为26 632 bp,大单拷贝区(large single copy, LSC)和小单拷贝区(small single copy, SSC)的长度分别为88 522 bp和18 405 bp;注释得到131个基因,包括85个蛋白质编码基因,36个tRNA基因,8个rRNA基因和2个假基因,其中18个基因包括一个或两个内含子;共检测到231个简单重复序列(short simple repeat, SSR)。此叶绿体基因组已在GenBank注册,序列号为KX752098。本研究为金莲花叶绿体分子标记研究提供了理论依据,有助于促进该物种分子育种、进化分析和系统发育的研究。     

荷花玉兰叶绿体全基因组高通量测序及结构解析

荷花玉兰是重要的药用、观赏及园林绿化植物.应用454高通量测序技术对荷花玉兰叶绿体全基因组进行测序,解析了其基因组结构,并与近缘物种基因组进行了比较分析.荷花玉兰叶绿体基因组全长为159623bp,两个反向互补重复区(IRs)长26563bp,被分隔的大单拷贝区(LSC)和小单拷贝区(SSC)长度分别为87757和18740bp.成功注释129个叶绿体基因,其中18个基因含有内含子.基因的种类、数目以及GC含量等与其他木兰科物种相类似.生物信息学分析获得218个SSR位点,大多位点富含A-T,具有碱基偏好性.木兰科物种的重复基序类型和丰度相对保守,有利于开发叶绿体基因组载体.木兰亚纲植物叶绿体基因组的大小及IR区边界的变化与ycf1的长度密切相关.采用30个物种叶绿体基因组的66个共有蛋白编码基因构建系统发育树,对木兰属在被子植物中的进化位置进行了探讨.荷花玉兰叶绿体全基因组序列的获得和结构解析对优良品种培育、叶绿体基因组工程、木兰科物种分子标记开发及系统发育关系的研究具有重要价值.     

苹果叶绿体基因组特征分析

苹果（Malus×domestica）是最重要的温带水果之一。为了能更好的了解本种的分子生物学基础．对已发布的苹果叶绿体全基因组序列进行了结构特征分析。结果显示苹果的叶绿体基因组全长为160068bp,具有典型的被子植物叶绿体基因组的环状四分体结构,包含大单拷贝区（LSC）,小单拷贝区（SSC）和两个反向互补重复区（IRs）,长度分别为88184bp,19180bp和26352bp。基因组共有135个基因（20个基因分布在反向互补重复区,因此整个基因组包含115个不同的基因）。按照功能进行分类,这115个基因包括81个蛋白质编码基因,4个rRNA编码基因和30个tRNA基因。其中,ycf15．ycf68和infA三个基因包含多个终止密码子,推测可能为假基因。苹果的基因组结构．基因顺序．GC含量和密码子使用偏好均与典型的被子植物叶绿体基因组类似。在苹果的叶绿体基因组中,共检测到30个大于30bp的重复序列,其中包括21串联重复,6个正向重复和3个反向重复序列;并检测到237个简单重复序列（SSR）位点,大部分的SSR位点都偏向于A或者T组成。此外,每10000bp非编码区平均分布有24个SSR位点,而编码区平均有5个SSR位点,表明SSRs在叶绿体基因组上的分布是不均匀的。本文对苹果叶绿体基因组序列特征的报道,将有助于促进该种的居群遗传学、系统发育和叶绿体基因工程的研究。     

五味子叶绿体基因组结构解析与比较分析

五味子是一种重要的药用植物.本研究通过Illumina HiSeq测序平台对五味子全基因组进行测序,完成了五味子叶绿体基因组的组装与结构解析,并与其他基部被子植物叶绿体基因组进行比较分析.五味子叶绿体基因组全长146730bp,GC含量为39.7%,由典型的4个区域组成,包括一个长单拷贝区、一个短单拷贝区和一对反向重复区(IR),其长度分别为95538、18270和16461 bp.共注释出113个基因,包括79个蛋白质编码基因、30个tRNA基因和4个rRNA基因.有4个蛋白质编码基因、5个tRNA基因和4个rRNA基因位于IR区.在五味子叶绿体基因组中共检测出47个简单重复序列和40个长重复序列.与一般被子植物叶绿体基因组相比,五味子叶绿体基因组IR区长度大约收缩10kb.IR区发生收缩的部分GC含量为37.4%,远小于IR区平均GC含量(45.7%).利用20个物种的53个共有蛋白质编码序列对五味子在被子植物中的系统发育位置进行了分析,结果表明五味子属与八角属为姊妹分支.对五味子叶绿体基因组序列进行分析,为五味子科物种鉴定、遗传多样性以及系统发育研究提供了数据基础.     

滇黄精叶绿体全基因组序列及其密码子使用偏性分析

为探究滇黄精(Polygonatum kingianum)叶绿体全基因组特征和密码子使用偏性,利用第二代测序技术对滇黄精嫩叶进行测序,再经组装与注释后得到其叶绿体基因组全序列,通过MISA、EMBOSS和CodonW等软件对滇黄精叶绿体全基因组的SSR位点、系统发育及密码子偏好性进行分析。结果表明,滇黄精完整叶绿体基因组长度为155 852 bp,基因组平均GC含量为37.7%,其大、小单拷贝区(LSC)长度分别为84 633和185 25 bp,反向重复区长度为26 347 bp,注释了132个基因,包括86个蛋白编码基因、38个tRNA基因和8个核糖rRNA基因。叶绿体基因组中共有69个SSR位点,绝大多数属于单碱基重复的A/T类型。系统发育分析表明滇黄精与格脉黄精(P. tessellatum)亲缘关系近,可能与分布地域有关。密码子偏好性分析表明,滇黄精叶绿体基因组密码子使用模式受到自然选择影响大于突变因素,最终确定9个最优密码子。因此, 滇黄精叶绿体基因组遗传结构和系统发育位置及其密码子偏倚的分析,为叶绿体基因工程研究提供理论依据。     

新型水果空心泡叶绿体基因组特征及其系统发育分析北大核心CSCD

为探究空心泡(Rubus rosaefolius)叶绿体基因组特征,本研究以空心泡为试验材料,采用Illumina NovaSeq平台进行高通量测序,获得空心泡完整的叶绿体基因组序列,并进行空心泡叶绿体基因序列特征和系统发育分析。结果表明:空心泡的完整叶绿体基因组总长度为155650 bp,具有典型的四分体结构,包括2个反向重复序列(各25748 bp)、1个大拷贝区(85443 bp)、1个小拷贝区(18711 bp)。空心泡叶绿体全基因组共鉴定出131个基因,包括86个蛋白质编码基因、37个tRNA基因和8个rRNA基因,全基因组的GC含量为36.9%。空心泡叶绿体基因组包含47个散在重复序列、72个简单重复序列(simple sequence repeating,SSR)位点,密码子偏好性为亮氨酸密码子,偏好使用A/U结尾的密码子。系统发育分析表明,空心泡与小叶悬钩子(Rubus taiwanicola)亲缘关系最近,其次是能高悬钩子(Rubus rubroangustifolius)和腺萼悬钩子(Rubus glandulosopunctatus)。空心泡的叶绿体基因组特征及其系统发育分析,为空心泡的遗传多样性研究和叶绿体开发利用提供理论依据。     

虎杖叶绿体基因组结构与变异分析

虎杖(Reynoutria japonica Houtt.)为蓼科(Polygonaceae)蓼族(Polygoneae)虎杖属(Reynoutria Houtt.)植物,是一种传统的中草药,具有利湿退黄、清热解毒、散瘀止痛、止咳化痰的功效。本研究采取高通量测序技术获得5个虎杖品种的叶绿体全基因组序列,并与NCBI已公布的蓼族何首乌(Fallopia multiflora)和金线草(Antenoron filiforme)等植物的叶绿体全基因组序列进行了基因组学和系统发育分析。通过基因组学分析发现,5种虎杖的叶绿体基因组大小有163 376 bp和163 371 bp两种情况,并呈现出典型的环状四分体结构,85 784 bp的一条较长的单拷贝区(large single-copy region,LSC),18 616 bp的一条较短的单拷贝区(small single-copy region,SSC),还有两条长度一致的反向重复区,分别为IRa区和IRb区相间隔分布。通过注释得到161个基因,其中蛋白编码基因106个,rRNA编码基因10个,tRNA编码基因45个。总GC含量为36.7...     

直刺变豆菜叶绿体全基因组及其特征

直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。     

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106259bp,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。     

Characterization of the Complete Chloroplast Genome of Apple (Malus × domestica,Rosaceae)*

Apple (Malus × domestica) is one of the most important temperate fruits. To better understand the molecular basis of this species, we characterized the complete chloroplast (cp) genome sequence downloaded from Genome Database for Rosaceae. The cp genome of apple is a circular molecule of 160068bp in length with a typical quadripartite structure of two inverted repeats (IRs) of 26352bp, separated by a small single copy region of 19180bp (SSC) and a large single copy region (LSC) of 88184bp. A total of 135 predicted genes (115 unique genes, and another 20 genes were duplicated in the IR) were identified, including 81 protein coding genes, four rRNA genes and 30 tRNA genes. Three genes of ycf15, ycf68 and infA contain several internal stop codons, which were interpreted as pseudogenes. The genome structure, gene order, GC content and codon usage of apple are similar to the typical angiosperm cp genomes. Thirty repeat regions (≥30bp) were detected, twenty one of which are tandem, six are forward and three are inverted repeats. Two hundred thirty seven simple sequence repeat (SSR) loci were revealed and most of them are composed of A or T, contributing to a distinct bias in base composition. Additionally, average 10000bp non coding region contains 24 SSR sites, while protein coding region contains five SSR sites, indicating an uneven distribution of SSRs. The complete cp genome sequence of apple reported in this paper will facilitate the future studies of its population genetics, phylogenetics and chloroplast genetic engineering.     

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5’ portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.     

Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L.

We determined the complete nucleotide sequence of the chloroplast genome of the leptosporangiate fern, Adiantum capillus-veneris L. (Pteridaceae). The circular genome is 150,568 bp, with a large single-copy region (LSC) of 82,282 bp, a small-single copy region (SSC) of 21,392 bp and inverted repeats (IR) of 23,447 bp each. We compared the sequence to other published chloroplast genomes to infer the location of putative genes. When the IR is considered only once, we assigned 118 genes, of which 85 encode proteins, 29 encode tRNAs and 4 encode rRNAs. Four protein-coding genes, all four rRNA genes and six tRNA genes occur in the IR. Most (57) putative protein-coding genes appear to start with an ATG codon, but we also detected five other possible start codons, some of which suggest tRNA editing. We also found 26 apparent stop codons in 18 putative genes, also suggestive of RNA editing. We found all but one of the tRNA genes necessary to encode the complete repertoire required for translation. The missing trnK gene appears to have been disrupted by a large inversion, relative to other published chloroplast genomes. We detected several structural rearrangements that may provide useful information for phylogenetic studies.     

The chloroplast genome from a lycophyte (microphyllophyte), <Emphasis Type="Italic">Selaginella uncinata</Emphasis>, has a unique inversion,transpositions and many gene losses

We determined the complete nucleotide sequence of the chloroplast genome of Selaginella uncinata, a lycophyte belonging to the basal lineage of the vascular plants. The circular double-stranded DNA is 144,170 bp, with an inverted repeat of 25,578 bp separated by a large single copy region (LSC) of 77,706 bp and a small single copy region (SSC) of 40,886 bp. We assigned 81 protein-coding genes including four pseudogenes, four rRNA genes and only 12 tRNA genes. Four genes, rps15, rps16, rpl32 and ycf10, found in most chloroplast genomes in land plants were not present in S. uncinata. While gene order and arrangement of the chloroplast genome of another lycophyte, Hupertzia lucidula, are almost the same as those of bryophytes, those of S. uncinata differ considerably from the typical structure of bryophytes with respect to the presence of a unique 20 kb inversion within the LSC, transposition of two segments from the LSC to the SSC and many gene losses. Thus, the organization of the S. uncinata chloroplast genome provides a new insight into the evolution of lycophytes, which were separated from euphyllophytes approximately 400 million years ago. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome

The nucleotide sequence of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome was completed (DQ119058). The circular double-stranded DNA, consisting of 155,527 bp, contained a pair of inverted repeat regions (IRa and IRb) of 25,187 bp each, which were separated by small and large single copy regions of 86,879 and 18,274 bp, respectively. The presence and relative positions of 113 genes (76 peptide-encoding genes, 30 tRNA genes, four rRNA genes, and three conserved open reading frames) were identified. The major portion (55.76%) of the C. sativus chloroplast genome consisted of gene-coding regions (49.13% protein coding and 6.63% RNA regions; 27.81% LSC, 9.46% SSC and 18.49% IR regions), while intergenic spacers (including 20 introns) made up 44.24%. The overall G-C content of C. sativus chloroplast genome was 36.95%. Sixteen genes contained one intron, while two genes had two introns. The expansion/contraction manner of IR at IRb/LSC and IR/SSC border in Cucumis was similar to that of Lotus and Arabidopsis, and the manner at IRa/LSC was similar to Lotus and Nicotiana. In total, 56 simple sequence repeats (more than 10 bases) were identified in the C. sativus chloroplast genome.     

阳春砂叶绿体全基因组解析及系统发育研究

以姜科(Zingiberaceae)豆蔻属(Amomum Roxb.)阳春砂(Amomum villosum)为试材,利用Illumina Hiseq 4000测序平台对阳春砂叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,以揭示阳春砂与其他姜科植物的进化关系及其在系统发育中的地位,为豆蔻属植物的物种鉴定提供理论依据。结果表明:(1)阳春砂叶绿体基因组全长164 069 bp,GC含量为36.1%,包括1对29 959 bp的反向重复区(IR)、一个大单拷贝区(LSC;88 798 bp)和一个小单拷贝区(SSC;15 353 bp);共注释得到133个基因,包括8个rRNA基因、38个tRNA基因和87个蛋白编码基因。(2)在阳春砂基因组中共检测到157个SSR位点,大部分SSR均由A和T组成;豆蔻属物种在基因组大小、IR边界区高度保守,核酸变异主要发生在LSC和SSC区。(3)最大似然法(Maximum Likelihood, ML)聚类分析显示,阳春砂与同属的爪哇白豆蔻(Amomum compactum)和白豆蔻(Amomum kravanh)亲缘关系最近,并且与山姜属(Alpinia Roxb.)也有较近的亲缘关系。     

Extensive Rearrangements in the Chloroplast Genome of <Emphasis Type="Italic">Trachelium caeruleum</Emphasis> Are Associated with Repeats and tRNA Genes

Chloroplast genome organization, gene order, and content are highly conserved among land plants. We sequenced the chloroplast genome of Trachelium caeruleum L. (Campanulaceae), a member of an angiosperm family known for highly rearranged genomes. The total genome size is 162,321 bp, with an inverted repeat (IR) of 27,273 bp, large single-copy (LSC) region of 100,114 bp, and small single-copy (SSC) region of 7,661 bp. The genome encodes 112 different genes, with 17 duplicated in the IR, a tRNA gene (trnI-cau) duplicated once in the LSC region, and a protein-coding gene (psbJ) with two duplicate copies, for a total of 132 putatively intact genes. ndhK may be a pseudogene with internal stop codons, and clpP, ycf1, and ycf2 are so highly diverged that they also may be pseudogenes. ycf15, rpl23, infA, and accD are truncated and likely nonfunctional. The most conspicuous feature of the Trachelium genome is the presence of 18 internally unrearranged blocks of genes inverted or relocated within the genome relative to the ancestral gene order of angiosperm chloroplast genomes. Recombination between repeats or tRNA genes has been suggested as a mechanism of chloroplast genome rearrangements. The Trachelium chloroplast genome shares with Pelargonium and Jasminum both a higher number of repeats and larger repeated sequences in comparison to eight other angiosperm chloroplast genomes, and these are concentrated near rearrangement endpoints. Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements.     

Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants

Recently, the complete chloroplast genome sequences of many important crop plants were determined, and this can be considered a major step forward toward exploiting the usefulness of chloroplast genetic engineering technology. Economically, cotton is one of the most important crop plants for many countries. To further our understanding of this important crop, we determined the complete nucleotide sequence of the chloroplast genome from cotton (Gossypium barbadense L.). The chloroplast genome of cotton is 160,317 base pairs (bp) in length, and is composed of a large single copy (LSC) of 88,841 bp, a small single copy (SSC) of 20,294 bp, and two identical inverted repeat (IR) regions of 25,591 bp each. The genome contains 114 unique genes, of which 17 genes are duplicated in the IRs. In addition, many open reading frames (ORFs) and hypothetical chloroplast reading frames (ycfs) with unknown functions were deduced. Compared to the chloroplast genomes from 8 other dicot plants, the cotton chloroplast genome showed a high degree of similarity of the overall structure, gene organization, and gene content. Furthermore, the sequences of the genes showed high degrees of identity at the DNA and amino acid levels. The cotton chloroplast genome was somewhat longer than the chloroplast genomes of most of the other dicot plants compared here. However, this elongation of the cotton chloroplast genome was found to be due mainly to expansions of the intergenic regions and introns (non-coding DNA). Moreover, these expansions occurred predominantly in the LSC and SSC regions.