Comparative chloroplast genomes of <Emphasis Type="Italic">Paris</Emphasis> Sect. <Emphasis Type="Italic">Marmorata</Emphasis>: insights into repeat regions and evolutionary implications

Background

Species of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. Thus, the availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. Here, we determined chloroplast genomes of Sect. Marmorata, and conducted the whole chloroplast genome comparison.

Results

This study presented detailed sequences and structural variations of chloroplast genomes of Sect. Marmorata. Over 40 large repeats and approximately 130 simple sequence repeats as well as a group of genomic hotspots were detected. Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P. verticillata. Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. And most of the genes underwent purifying selection, whereas photosynthetic genes experienced a relatively relaxed purifying selection.

Conclusions

Repeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. Marmorata and other species in subgenus Daiswa. Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. Therefore, this study enhances the understanding about evolution of Sect. Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect. Marmorata.

     

桃儿七叶绿体比较基因组学分析

为探究桃儿七(Sinopodophyllum hexandrum)不同叶绿体基因组特征,本研究以桃儿七5个叶绿体基因组为研究对象,借助生物信息学工具进行基因组图谱构建、重复序列分析、密码子偏好分析、反向重复序列区(inverted repeat, IR)/单拷贝区(single-copy, SC)边界分析、基因组序列比较分析及系统发育分析。结果表明:桃儿七5个叶绿体基因组全长为157 203–157 940 bp,为典型的叶绿体四分体结构,共注释出133–137个基因,说明桃儿七叶绿体基因组具有多样性。桃儿七不同叶绿体基因组简单重复序列(simple sequence repeat, SSR)位点不同,单核苷酸A/T占主要优势,散在重复序列包括正向重复、回文重复和反向重复3类。密码子偏好分析显示有效密码子(effective number of codon,ENc)值为51.14–51.17,密码子偏好性弱,GC与GC3s所占比例小于50%,密码子偏向使用A和U碱基并且以A和U碱基结尾。桃儿七5个叶绿体基因组IR/SC边界和基因组序列均比较保守。系统发育分析结果表明桃儿七和北美桃儿七亲...     

沙枣叶绿体全基因组序列及其使用密码子偏性分析

该研究以2株野生沙枣(Elaeagnus angustifolia Linn.)嫩枝经温室水培后的嫩叶为材料,采用CTAB法分别提取总DNA,并利用第二代测序技术进行总DNA从头测序,组装后得到2株沙枣叶绿体基因组全序列,并详细分析了其蛋白质编码基因密码子使用的偏好性及其原因,为沙枣叶绿体基因工程和分子系统进化等研究奠定基础。结果显示:(1)组装得到沙枣叶绿体基因组序列全长150 546 bp,由长度为81 113 bp的长单拷贝(LSC)区域和25 494 bp的短单拷贝(SSC)区域,以及1对分隔开它们的长18 445 bp的反向重复序列(IRS)组成;注释共得到132个基因,包括86个蛋白编码基因、38个tRNA基因和8个rRNA基因。(2)沙枣叶绿体基因组蛋白编码基因密码子的第三位碱基GC含量(GC_3)为28.47%,明显低于整个叶绿体基因组GC含量(37%),也低于第一位(GC_1)和第二位(GC_2)碱基的GC含量,说明密码子对AT碱基结尾有偏好性;其中, UCU、CCU、UGU、GCU、CUU、GAU、UCA和UAA为最优密码子。(3)同义密码子相对使用频率(RSCU)分析发现,影响密码子使用模式的因素并不单一,密码子的偏好性受到突变、选择及其他因素的共同影响,并且自然选择表达引起的序列差异比突变对密码子偏好性的影响要显著;中性绘图分析、有效密码子数(ENC-plot)分析和奇偶偏好性(PR2-plot)分析表明,沙枣叶绿体基因组使用密码子的偏性受选择的影响更大。(4)通过最大似然法、最大简约法和贝叶斯方法对胡颓子科6个物种和1个枣的叶绿体基因序列构建系统发育树,与它们使用密码子偏性聚类的结果一致,表明叶绿体基因组使用密码子偏性与物种的亲缘关系相关。     

Chloroplast DNA codon use: Evidence for selection at the psb A locus based on tRNA availability

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.     

Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages

In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity among the various genomes are discussed. Received: 6 June 1997 / Accepted: 24 July 1997     

Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species

A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm speciesOryza sativa, Zea mays, Triticum aestivum andArabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes inO. sativa, Z. mays, andT. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.     

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。     

An annotated catalogue of salivary gland transcripts in the adult female mosquito, Ædes ægypti*

Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comParative analyses. In comParative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

Results

The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in s of abundance and length and most contain repeat motifs based on A and T nucleotides.

Conclusion

SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.     

极小种群植物川柿叶绿体基因组特征与系统发育分析（附录）

川柿(Diospyros sutchuensis)为极小种群和国家重点保护野生植物,分布范围狭窄,种群数量极少。目前,川柿基因组信息缺乏,在柿属(Diospyros)中的系统亲缘关系不明确。该研究通过Illumina平台对川柿叶绿体基因组进行测序,应用Getorganellev1.7.3.4和PGA软件对基因组进行组装和注释,使用DnaSP6.12.03软件进行多序列对比分析,并使用REPuter、Tandem Reapeats Finder和MISA软件进行重复序列分析,使用CodonW1.4和EasyCodemL软件分别进行密码子偏好性和选择压力分析。同时,基于4个不同的叶绿体基因组序列数据集,使用IQtree软件分析川柿与11个柿属物种的系统发育关系。结果表明:(1)川柿叶绿体基因组全长157 917 bp,包含1对26 111 bp的反向重复区、大单拷贝区(87 303 bp)和小单拷贝区(18 392 bp),GC碱基含量为37.4%。(2)川柿叶绿体基因组共注释到113个基因,包括79个蛋白编码基因、30个tRNA基因和4个rRNA基因; 共检测到49个长重复序列、27个串联重复序列和34个简单重复序列; 蛋白编码基因中高频密码子31个,多数密码子末位碱基为A或U,编码亮氨酸的密码子使用最多; 基因组编码区比非编码区更为保守,10个高变热点区域可作为潜在的分子标记; 蛋白编码基因中有8个基因(ndhB、ndhG、ndhI、rbcL、rpoB、petB、petD、rps12)受到正选择压力。(3)系统发育分析显示,川柿与老鸦柿(D. rhombifolia)和乌柿(D. cathayensis)亲缘关系最为密切,它们与海南柿(D. hainanensis)共同形成一个单系分支。该研究结果既为川柿及柿属种质资源鉴定、遗传多样性保护以及种群恢复等提供了叶绿体基因组资源,也为阐明川柿的系统进化提供了重要的分子信息。     

Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions

Background

Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.

Results

We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN).

Conclusions

IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.

     

红锥叶绿体基因组特征及系统发育分析

为确定红锥(Castanopsis hystrix)叶绿体基因组的结构组成情况,判定其在锥属中的进化位置及与同锥属叶绿体基因组的区别,为锥属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina HiSeq 2500测序平台对红锥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,并利用R、Python、MISA、CodonW和MEGA 6等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、简单重复序列(simple sequence repeat,SSR)位点和系统发育进行分析。结果表明红锥叶绿体基因组大小为153754 bp,呈现四分体结构;共拥有130个基因,包含85个编码基因、37个tRNA基因和8个rRNA基因;通过密码子偏好性分析,平均有效密码子数为55.5,说明其密码子随机性强、偏好性低;通过SSR及长重复片段分析,检测到45个重复序列及111个SSR位点;与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高;此外,系统发育分析发现红锥与海南锥聚为一支,关系密切。本研究得到了红锥的叶绿体基因组基本情况与系统发育位置,为红锥的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。     

猴樟叶绿体基因组特征分析

猴樟(Cinnamomum bodinieri)枝叶含有丰富的精油,是重要的园林绿化树种和经济树种,但目前有关猴樟基因组学的研究报道不多。为揭示猴樟叶绿体基因组特征及系统发育关系,该文基于高通量测序平台进行测序,从头组装了完整的猴樟叶绿体基因组,并对其基因组结构、基因构成及序列重复、密码子使用偏好性以及系统发育进行分析,结合樟亚科主要属物种叶绿体基因组数据构建系统发育树。结果表明:(1)猴樟叶绿体基因组全长152 727 bp,包括一对20 132 bp的反向重复(IRs)区、93 605 bp的大单拷贝(LSC)区和18 858 bp的小单拷贝(SSC)区,总GC含量为39.13%。(2)该基因组共编码127个基因,包括83个蛋白质编码基因(PCGs)、36个转运RNA基因(tRNAs)和8个核糖体RNA基因(rRNAs); 共鉴定出92个SSR位点,其中大部分是A/T组成的单核苷酸重复序列; 密码子适应指数(CAI)为0.166,有效密码子数(ENc)为54.68; 猴樟与近缘种的叶绿体基因组主要在IR区和2个SC区边界上存在一定的差异。(3)24种樟亚科植物的系统发育树显示,猴樟与樟树亲缘关系最近,同时支持了樟属-甜樟属分支(Cinnamomum-Ocotea Clade)、月桂属-新木姜子属分支(Laurus-Neolitsea Clade)、润楠属-鳄梨属分支(Machilus-Persea Clade)的建立。该研究丰富了猴樟遗传资源信息,进一步确定了樟亚科主要属的系统发育地位。     

藏波罗花叶绿体基因组分析

藏波罗花（Incarvillea younghusbandii Sprague）是一种传统的补益类中药。其根作草药使用,用于滋补强壮,治产后少乳、久病虚弱、头晕、贫血等症。但目前关于藏波罗花分子遗传信息的研究很少。本研究基于高通量测序技术对藏波罗花叶绿体基因组进行测序、组装和注释,并对其序列特征、密码子偏好性、重复序列、系统发育和分化时间进行分析。结果表明,藏波罗花叶绿体基因组全长为159 323 bp,包含1个大单拷贝区（80 197 bp）、1个小单拷贝区（9 030 bp）和2个反向重复区（35 048 bp）;共注释出120个基因,包括77个蛋白编码基因、8个rRNA基因和35个tRNA基因;密码子偏好性分析显示,AAA是藏波罗花叶绿体基因组中使用最频繁的密码子;从藏波罗花叶绿体基因组中共检测到42个简单重复序列（simple sequence repeats,SSR）;系统发育分析表明,藏波罗花与密生波罗花（Incarvillea compacta）的亲缘关系最近,且在大概466万年前产生分化。本研究对藏波罗花相关资源的科学保护和开发具有重要的现实意义,也可以为后续角蒿属（Incarvillea）的物种鉴定、紫葳科（Bignoniaceae）的种群遗传多样性研究提供基本的遗传资源。     

Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identified 33–45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

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。     

Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that psbA has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant psbA gene during Angiosperm evolution.     

Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis

Pairwise comparison of whole plastid and draft nuclear genomic sequences of Arabidopsis thaliana and Oryza sativa L. ssp. indica shows that rice nuclear genomic sequences contain homologs of plastid DNA covering about 94 kb (83%) of plastid genome and including one or more full-length intact (without mutations resulting in premature stop codons) homologues of 26 known protein-coding (KPC) plastid genes. By contrast, only about 20 kb (16%) of chloroplast DNA, including a single intact plastid-derived KPC gene, is presented in the nucleus of A. thaliana. Sixteen rice plastid genes have at least one nuclear copy without any mutation or with only synonymous substitutions. Nuclear copies for other ten plastid genes contain both synonymous and non-synonymous substitutions. Multiple ESTs for 25 out of 26 KPC genes were also found, as well as putative promoters for some of them. The study of substitutions pattern shows that some of nuclear homologues of plastid genes may be functional and/or are under the pressure of the positive natural selection. The similar comparative analysis performed on rice chromosome 1 revealed 27 contigs containing plastid-derived sequences, totalling about 84 kb and covering two thirds of chloroplast DNA, with the intact nuclear copies of 26 different KPC genes. One of these contigs, AP003280, includes almost 57 kb (45%) of chloroplast genome with the intact copies of 22 KPC genes. At the same time, we observed that relative locations of homologues in plastid DNA and the nuclear genome are significantly different.     

Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes

Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.     

长爪栘[木衣]叶绿体基因组特征系统发育及密码子偏好性分析

长爪栘[木衣](Docynia longiunguis Q.Luo & J.L.Liu)是我国特有的栘[木衣]属植物,具有较高的食药用价值.对其叶绿体基因组进行分析,有助于阐明栘[木衣]属内的系统发育关系,为长爪栘[木衣]资源的开发利用及进一步研究奠定基础.结合其近缘种云南移[木衣]叶绿体基因组数据,在进行全序列比对后...