Complete structure of the chloroplast genome of a legume, Lotus japonicus.

The nucleotide sequence of the entire chloroplast genome (150,519 bp) of a legume, Lotus japonicus, has been determined. The circular double-stranded DNA contains a pair of inverted repeats of 25,156 bp which are separated by a small and a large single copy region of 18,271 bp and 81,936 bp, respectively. A total of 84 predicted protein-coding genes including 7 genes duplicated in the inverted repeat regions, 4 ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acids species were assigned on the genome based on similarity to genes previously identified in other chloroplasts. All the predicted genes were conserved among dicot plants except that rpl22, a gene encoding chloroplast ribosomal protein CL22, was missing in L. japonicus. Inversion of a 51-kb segment spanning rbcL to rpsl6 (positions 5161-56,176) in the large single copy region was observed in the chloroplast genome of L. japonicus. The sequence data and gene information are available on our World Wide Web database at http://www.kazusa.or.jp/en/plant/database.html.     

The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis

The complete nucleotide sequence of mulberry (Morus indica cv. K2) chloroplast genome (158,484 bp) has been determined using a combination of long PCR and shotgun-based approaches. This is the third angiosperm tree species whose plastome sequence has been completely deciphered. The circular double-stranded molecule comprises of two identical inverted repeats (25,678 bp each) separating a large and a small single-copy region of 87,386 bp and 19,742 bp, respectively. A total of 83 protein-coding genes including five genes duplicated in the inverted repeat regions, eight ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acids, were assigned on the basis of homology to predicted genes from other chloroplast genomes. The mulberry plastome lacks the genes infA, sprA, and rpl21 and contains two pseudogenes ycf15 and ycf68. Comparative analysis, based on sequence similarity, both at the gene and genome level, indicates Morus to be closer to Cucumis and Lotus, phylogenetically. However, at genome level, inclusion of non-coding regions brings it closer to Eucalyptus, followed by Cucumis. This may reflect differential selection pressure operating on the genic and intergenic regions of the chloroplast genome.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Communicated by Y. Tsumura     

The complete structure of the cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) chloroplast genome: Its composition and comparative analysis

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.     

The chloroplast genome of the “basal” angiosperm Calycanthus fertilis – structural and phylogenetic analyses

The nucleotide sequence of the complete chloroplast genome of a basal angiosperm, Calycanthus fertilis, has been determined. The circular 153337 bp long cpDNA is colinear with those of tobacco, Arabidopsis and spinach. A total of 133 predicted genes (115 individual gene species, 18 genes duplicated in the inverted repeats) including 88 potential protein-coding genes (81 gene species), 8 ribosomal RNA genes (4 gene species) and 37 tRNA genes (30 gene species) representing 20 amino acids were identified based on similarity to their homologs from other chloroplast genomes. This is the highest gene number ever registered in an angiosperm plastome. Calycanthus fertilis cpDNA also contains a homolog of the recently discovered mitochondrial ACRS gene. Since no gene transfer from mitochondria to the chloroplast has ever been documented, we investigated the evolutionary affinity of this gene in detail. Phylogenetic analysis of the protein-coding subset of the plastome suggests that the ancient line of Laurales emerged after the split of the angiosperms into monocots and dicots. Calycanthus fertilis Walter var. ferax (Michy.) Rehder is a synonym of C. floridus L. var. glaucus (Willd.) Torr. & A. Gray.Data deposition: The sequence reported in this paper has been deposited in the EMBL database (accession no. AJ428413).     

Complete mitochondrial genome of the Bewick's swan Cygnus columbianus bewickii (Aves, Anseriformes, Anatidae)

The mitochondrial genome of Bewick's swan Cygnus columbianus bewickii was completely sequenced and then the resultant data were compared with those of the whistling swan Cygnus columbianus columbianus. The complete mitochondrial genome sequence of C. c. bewickii was 16,727?bp in length and its gene arrangement pattern, gene content, and genome organization were identical to those of Cygnus species. The similarities of nucleotide and amino acid sequences between the two swans were 99.1% and 99.6%, respectively. Out of the 13 protein-coding genes and 2 rRNA genes, COIII showed the lowest nucleotide sequence similarity with 98.0%. On the other hand, in amino acid sequence similarities, both COII and ATP6 showed the lowest with 98.7% in common. The control region has the 97.8% nucleotide sequence similarity.     

Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones.

To deduce the entire sequence of the top arm of the Arabidopsis thaliana chromosome 3, the sequence determination was performed on a total of 90 P1, TAC and BAC clones chosen according to our sequencing strategy. Sequence features of the resulting 4,251,695 bp regions were analyzed with various computer programs for similarity search and gene modeling. As a result, a total of 941 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4210 bp. Introns were observed in 73% of the genes, and the average number per gene and the average length of the introns were 3.6 and 159 bp, respectively. These sequence features are essentially identical to those of chromosomes 3 and 5 in our previous reports. The regions also contained 14 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/kaos/.     

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.     

Structural Analysis ofArabidopsis thaliana Chromosome 5. VI. Sequence Features of the Regions of 1,367,185 bp Covered by 19 Physically Assigned P1 and TAC Clones

Nineteen Pl and TAC clones, which have been mapped on the finephysical map of the Arabidopsis thaliana chromosome 5, weresequenced according to the shotgun-based strategy, and theirstructural features were analysed. The total length of the regionssequenced in this study was 1,367,185 bp. Combining this withthe regions covered by 90 P1 and TAC clones proviously reported,the total length of chromosome 5 sequenced to date becomes 8,058,855bp. On the basis of similarity search against protein and ESTdatabases and gene modeling with computer programs, a totalof 330 potential protein-coding regions were identified, bringingan average density of the genes to approximately one gene per4.1 kb. Introns were identified in 81.0% of the potential proteingenes for which the entire gene structure was predicted, withan average number per gene of 4.2 and an average length of theintrons of 180 bp. The RNA-coding genes identified were 9 tRNAgenes corresponding to 8 amino acid species and 2 genes forU2 nuclear RNA. These sequence features are essentially identicalto those in the previously reported sequences. The sequencedata and gene information are available on the World Wide Webdatabase KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.     

Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones.

In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential protein-coding genes in the 10,154,580 bp regions, which are covered by 142 P1 and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 P1 and TAC clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available on the database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.     

青藏高原特有种-藏扇穗茅叶绿体基因组测序及序列分析

藏扇穗茅（Littledalea tibetica）是禾本科（Poaceae）雀麦族（Bromeae）中一个具有重要生态价值的多年生高山特有种,主要分布于青藏高原及其毗邻地区。本文采用基于第二代高通量测序平台的Illumina MiSeq技术,对青藏高原特有种—藏扇穗茅进行了叶绿体基因组测序,首次建立了雀麦族物种的标准测序流程;同时,以其近缘物种—黑麦草（Lolium perenne）的叶绿体基因组序列作为参考,组装获得它的叶绿体基因组序列。结果表明,藏扇穗茅叶绿体基因组序列全长136 852 bp,GC含量为38.5%,呈典型的四段式结构,其中大（LSC）、小（SSC）单拷贝区大小分别为80 970和12 876 bp,反向互补重复区（IR）大小为21 503 bp,共注释得到141个基因,包含95个蛋白编码基因、38个tRNA基因和8个rRNA基因,主要分布于大单拷贝区和小单拷贝区。同时,基于藏扇穗茅和其它30种禾本科植物叶绿体基因全序列构建的系统发育树显示,藏扇穗茅与早熟禾亚科中小麦族植物亲缘关系较近。     

Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales

The complete chloroplast genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae, Liliales) was mapped using polymerase chain reaction and the Sanger method. The circular double-stranded DNA was a typical quadripartite structure consisting of two inverted repeated regions (27,397 bp), a small single copy region (18,205 bp), and a large single-copy region (81,646 bp), with a total length of 154,645 bp. The genome consisted of 137 coding genes, including 91 protein-coding genes, 38 distinct tRNA, and 8 rRNA genes. The ycf15 and ycf68 genes had several internal stop codons interpreted as pseudogenes. The inverted repeat (IR) region expanded to part of the rps3 gene in the junction between large single-copy and IRA regions in C. japonica. We designed 785 primers, of which 481 were used to map the entire chloroplast genome of C. japonica. Primers were compared with the complete chloroplast sequence of Smilax china (Smilacaceae) to identify primers that could be used for other Liliales members and whole chloroplast genome sequencing. Of the primers used for C. japonica, 398 could be used with other smaller species within the order.     

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。     

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。     

Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones.

Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/kaos/.     

Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC

Blumea balsamifera (L.) DC., a medicinal plant with high economic value in the Asteraceae family, is widely distributed in China and Southeast Asia. However, studies on the population structure or phylogenetic relationships with other related species are rare owing to the lack of genome information. In this study, through high-throughput sequencing, we found that the chloroplast genome of B. balsamifera was 151,170 bp in length, with a pair of inverted repeat regions (IRa and IRb) comprising 24,982 bp, a large single-copy (LSC) region comprising 82,740 bp, and a small single-copy (SSC) region comprising 18,466 bp. A total of 130 genes were identified in the chloroplast genome of B. balsamifera, including 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes; furthermore, sequence analysis identified 53 simple sequence repeats. Whole chloroplast genome comparison indicated that the inverted regions (IR) were more conserved than large single-copy and SSC regions. Phylogenetic analysis showed that B. balsamifera is closely related to Pluchea indica. Conclusively, the chloroplast genome of B. balsamifera was helpful for species identification and analysis of the genetic diversity and evolution in the genus Blumea and family Asteraceae.     

The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region

The nucleotide and amino acid sequences and the gene order of the mitochondrial genome are highly informative for studying phylogeny, population genetics, and phylogeography. This study determined the complete mitochondrial genome of the caprellid species Caprella scaura. The mitochondrial genome of C. scaura has a total length of 15,079 bp, with an AT content of 66.43%. The mitochondrial genome contains typical gene components, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. In comparison with the mitochondrial genome of a gammarid, some distinct characteristics were found. For example, the order of the two conserved gene blocks is inverted between Gammaridea and C. scaura. In addition, two copies of almost identical control regions were found in the mitochondrial genome of C. scaura. These unique characteristics will be useful for determining the evolutionary history of the Caprellidea.     

小檗科科尔切斯淫羊藿叶绿体全基因组研究

小檗科科尔切斯淫羊藿(Epimedium pinnatum Fisch.ex DC.)是分布于高加索地区的一种具有观赏和药用价值的多年生草本植物.本研究首次报道了科尔切斯淫羊藿的叶绿体全基因组序列.结果显示:科尔切斯淫羊藿叶绿体基因组全长为156155 bp,GC含量为38.82％;由一个大的单拷贝区(LSC,8942...     

The chloroplast genome sequence from <Emphasis Type="Italic">Eugenia uniflora</Emphasis>, a Myrtaceae from Neotropics

Eugenia uniflora is a plant native to tropical America that holds great ecological and economic importance. The complete chloroplast (cp) genome sequence of Eugenia uniflora, a member of the Neotropical Myrtaceae family, is reported here. The genome is 158,445 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,459 bp) and small (SSC, 18,318 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 26,334 bp). It contains 111 unique genes, including 77 protein-coding genes, 30 tRNAs and 4 rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Comparison of the entire cp genomes of E. uniflora L. and three other Myrtaceae revealed an expansion of 43 bp in the intergenic spacer located between the IRA/large single-copy (LSC) border and the first gene of LSC region. Simple sequence repeat (SSR) analysis revealed that most SSRs are AT rich, which contribute to the overall AT richness of the cp genome. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the noncoding regions. Phylogenetic analysis among 58 species based on 57 cp genes demonstrated a closer relationship between E. uniflora L. and Syzygium cumini (L). Skeels compared to the Eucalyptus clade in the Myrtaceae family. The complete cp genome sequence of E. uniflora reported here has importance for population genetics, as well as phylogenetic and evolutionary studies in this species and other Myrtaceae species from Neotropical regions.     

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。