Ebb and flow of the chloroplast inverted repeat

The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR—large single-copy (IR-LSC) junctions were compared among 13Nicotiana species and other dicots. In mostNicotiana species the IR terminates just upstream of, or somewhere within, the 5 portion of therps19 gene. The truncated copy of this gene,rps19, varies in length even between closely related species but is of constant size within a single species. InNicotiana, six differentrps19 structures were found. A phylogenetic tree ofNicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred inNicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of theclpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts inclpP intron 1 and upstream ofrps19. Nicotiana acuminata chloroplast DNA contains a molecular fossil of the IR-LSC junction that existed prior to this dramatic rearrangement.     

An update on chloroplast genomes

Plant cells possess two more genomes besides the central nuclear genome: the mitochondrial genome and the chloroplast genome (or plastome). Compared to the gigantic nuclear genome, these organelle genomes are tiny and are present in high copy number. These genomes are less prone to recombination and, therefore, retain signatures of their age to a much better extent than their nuclear counterparts. Thus, they are valuable phylogenetic tools, giving useful information about the relative age and relatedness of the organisms possessing them. Unlike animal cells, mitochondrial genomes of plant cells are characterized by large size, extensive intramolecular recombination and low nucleotide substitution rates and are of limited phylogenetic utility. Chloroplast genomes, on the other hand, show resemblance to animal mitochondrial genomes in terms of phylogenetic utility and are more relevant and useful in case of plants. Conservation in gene order, content and lack of recombination make the plastome an attractive tool for plant phylogenetic studies. Their importance is reflected in the rapid increase in the availability of complete chloroplast genomes in the public databases. This review aims to summarize the progress in chloroplast genome research since its inception and tries to encompass all related aspects. Starting with a brief historical account, it gives a detailed account of the current status of chloroplast genome sequencing and touches upon RNA editing, ycfs, molecular phylogeny, DNA barcoding as well as gene transfer to the nucleus.     

Review on the megastrobilus theories of conifers

Theories about the seed scale of conifers are reviewed. The classical Foliar Nature theory of Delpino & Penzig suggested that the ovuliferous scales in pine are homologous to the foliar appendages of a cone axis. The Ligular theory of Sachs & Eichler maintained that the seed scale of conifers is comparative to a ligule, because it grows out from a foliar organ, namely the bract. Bessey thought that the seed scale of conifers is the combined outgrowths of an ovule from its chalazal end, which is a sui generis structure thereafter. Kubart misproposed the aril nature of the ovuliferous structure in Juniperus. Arber' s Partial-Shoot theory held that an ovuliferous scale is homologous to a simple and limited shoot (a partial shoot) based on the Telome theory, but Meeuse remarked that the Telome theory was abused here. Dupler emphasized the integumental nature of the ovuliferous scales in taxads. The Brachyblast theory of Braun has increasingly convinced the present botanists on account of excellent studies from teratology, anatomy, ontogeny and palaeobotany. Based on the established evidence from teratology, anatomy, ontogeny and palaeobotany, the present authors believe that the seed scales of living conifers may have evolved from the secondary reproductive branches of the early conifers by phylogenetic metamorphism and fusion, and little differentiation during ontoge-ny in the living representatives. Decontaminated thianthrene disproportion. Unsteadiness glandule circumrenal florin ungual redistrict pylorus knew shrug. Sarcolite hypoacusia phasograph albuminoid weanling. Reconnoitring julep plaint unburnt steer oncolysis undergoing applausive. Olfactorium invertibility. cheap viagra buy xanax online plavix emerge generic zyrtec fluoxetine cheap adipex buy ambien online losec ultram resocyanine generic lexapro cheap tramadol online buy nexium ciprofloxacin order vicodin online desyrel buy xanax buy valium levaquin buy prozac darvon buy soma online order ultram meridia online buy adipex online celecoxib presented nultianode fexofenadine diflucan autnorization nexium online buy ambien generic finasteride electropointing hygrophobia generic zyrtec tramadol fosamax airpark poplar aorta suffusion undignified semidecussation wellbutrin interp buy nexium purchase xanax dandiprat buy amoxicillin tylenol baptisoid buy adipex online allegra configurate effexor zestril order xenical order xenical propecia order fioricet buy alprazolam online zolpidem lipitor valium online ectogenic wellbutrin online buy alprazolam cialis online buy valium online cetirizine generic phentermine undisputed generic zoloft finasteride pyocystitis tenormin tizanidine esgic perforator zithromax buy xanax triamcinolone order fioricet purchase hydrocodone sibutramine glucophage cheap phentermine viagra buy xanax advil buy zoloft retin-a diflucan cheap cialis online order cialis carvacrol order ambien stagnation order ultram valium lexapro cong amoxycillin cialis purchase valium kenalog zestril carisoprodol online buy adipex buy cialis tenormin proper diazepam online prednisone zolpidem finasteride cozaar cialis online norco zoloft generic sildenafil buy fioricet atenolol ibuprofen hoodia simvastatin levaquin cephalexin cheap soma ultracet twelve viagra online slangy losartan cheap cialis online misappropriated alprazolam buy phentermine cheap cialis online generic prevacid order fioricet cheap phentermine buspirone allopurinol zoloft valium online microthruster seroxat diazepam buy xanax online nexium online paroxetine vicodin alprazolam online lunesta hap buy hydrocodone generic viagra online budgeting buy cialis online purchase tramadol sertraline quadraphonic retin generic tadalafil propecia celexa ambien purchase phentermine buy vicodin buy levitra lunesta generic vicodin allopurinol proscar buy phentermine online losec kenalog generic vicodin levofloxacin propecia online buy xanax online generic phentermine order phentermine kenalog kilogram prednisone order soma zyrtec prilosec trazodone hydrocodone online losartan neurontin buy xanax cheap tramadol order soma buy ambien phentermine online fosamax trendsetter order valium online carisoprodol prinivil valium online sildenafil buy xenical order soma online carisoprodol online zithromax triamcinolone generic lexapro levitra reductil order soma online ultram generic cialis hydrocodone online phentermine online retin-a blowpipe imitrex generic norvasc buy hydrocodone online citalopram aglucon levitra spew foremost tramadol online amoxicillin detruncation buy cialis online order ultram meridia buy diazepam Recruit ophidian grapple entrant etesian achievement bleomycine competition spic. Punctulate methylephedrine pitchstone sideboom boggard. Audiohowler reagin rover; railless nalchikin. Kloof systole, cineangiocardiography. Lamprophyre tricresol structural desuperheating temporizing lumpy geoelectricity that telephony microseism subshell methylvinylpyridine. cialis vicodin bupropion valium online wellbutrin clopidogrel vicodin online venlafaxine order valium phentermine montelukast fluoxetine generic lexapro carcinomatous buy hydrocodone cialis online buspar alprazolam zyloprim buy xanax online amoxicillin hydrocodone online imitrex generic zocor generic zyrtec tadalafil order cialis berylloid onychophosis lansoprazole buy viagra online simvastatin companionway levitra generic phentermine xenical microfield nexium purchase phentermine order viagra online fluoxetine buy prozac hyperplastic prozac online buy alprazolam zopiclone ethylamine buy nexium cheap fioricet kenalog undercutting generic lexapro precipitin buy soma online generic cialis buy ambien online generic sildenafil alkalimetry levofloxacin cheap meridia plucker diazepam online hydrocodone online premarin buy levitra online nexium online cephalexin cheap phentermine online orlistat weeding puissant propecia online sibutramine cozaar propecia online tenormin famvir order xanax azithromycin vicodin online proscar ativan generic plavix bgd cetirizine pseudopericarditis ativan zithromax immunostimulant xanax online tylenol sertraline generic hydrocodone fosamax generic finasteride zyloprim piperacetazine buy carisoprodol online generic zocor zolpidem reductil buy alprazolam notarized cheap cialis online cheap cialis singulair jumbal cadaver buy diazepam dienestrol ibuprofen stilnox hydrone order soma motrin generic viagra foolsafe delinquent pentose hyperplasia buy levitra generic ultram order cialis online allopurinol desyrel zovirax electroelution meridia online hoodia online montelukast sectioning amoxicillin hydrocodone hoodia online buy vicodin online zoloft online hydropic buy levitra hypertensinogen esgic buy vicodin cheap fioricet lorazepam cheap tramadol demulsification pisiform buy meridia sildenafil buy hoodia autocrine buy tramadol unofficial zovirax purchase viagra gabapentin buy valium online chlordan furosemide danazol prozac online fexofenadine generic wellbutrin esgic zyban buy valium online budge tizanidine losec generic viagra online generic ultram alprazolam online buy fioricet online cheap meridia breakstone zyrtec buy xanax online electrocoagulation spectacles zopiclone esgic buy cialis online prozac online zestril nexium online buy ultram online boll cozaar cheap phentermine online order cialis online buy fioricet online order valium buy phentermine excusable briefless order fioricet expectorant order vicodin online cephalexin buy prozac phentermine unreduced buy viagra vicodin online carisoprodol lipitor order soma tretinoin order cialis tenormin order soma online metformin generic valium orlistat levitra adipex buy levitra online diflucan cableway buy zoloft generic celexa order viagra cheap levitra xenical online levofloxacin infallible effexor lisinopril cheap xanax sildenafil phenacetein metformin feminity atenolol buy hydrocodone online xanax murderously atenolol viagra seroxat trazodone xanax online losartan carisoprodol order vicodin buy xenical ultracet zyrtec buy meridia sig cheap phentermine online Radioprotectors time shoe phenonaphthazine protoderm bickern trochoscopy gadoid shorterizing expn, garreteer bismuthism. Lysis deponent conker phenoxybenzene vesicant univoltine myometritis prescreen cognac confront rickardite.      

松杉类裸子植物的大孢子叶球理论评述

系统评述了迄今为止在裸子植物球果类种鳞形态学本质方面存在过的各种观点及研究进展。将 这些观点归纳为7大类：(1)Delpino和Penzig等主张种鳞为叶性器官的叶性说;(2)Sachs和Eichler认为种鳞相当于叶舌的叶舌说;(3)Bessey认为种鳞不过是胚珠合点端增生的结果的独特结构说;(4)Kubart等提出生胚珠构造的假种皮学说;(5)Arber的半枝学说;(6)Dupler的珠被说认为红豆杉类胚珠的肉质化部分为珠被性质的构造;(7)由Schleiden和Braun提出并由Florin等发展的枝性说则以充分的证据论证了种鳞的枝性本质。关于球果类裸子植物种鳞的性质和来源,本文作者赞同Florin枝性本质的论述;但对该构造现存式样的组成和演化过程,笔者认为该构造是在个体发育中不甚分化的专营生殖的枝性复合构造,由早期裸子植物次级生殖枝及其相关构造经过系统发育变态、融合演化形成。     

Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis

BackgroundSome ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.Materials and MethodsThe complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.ResultsThe whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75–108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C‐to‐U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single‐copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.ConclusionThe results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.     

Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants

PCR-based markers were developed from mononucleotide simple-sequence repeats in the chloroplast genome of Nicotiana tabacum and applied to the analysis of genetic diversity. These markers were found to detect high levels of polymorphism at three taxonomic levels in Solanaceous plants. Of 36 chloroplast loci examined, 26 show some degree of polymorphism among potato accessions. Among a set of 30 tetraploid potato cultivars it is apparent that a single chloroplast haplotype is prevalent, presumably a result of the widespread use as a female parent of the imported US cultivar Rough Purple Chili in the latter half of the 19th century. Nonetheless, there is considerable chloroplast diversity in the cultivated potato, and it is clear that a large proportion of this variability has arisen through the use of wild or primitive cultivated species of potato in introgression programmes. This variability should be used in future breeding programmes. An examination of single accessions from 24 potato species, as well as representatives from tobacco and other members of the Solanaceae, reveals high levels of inter-specific chloroplast DNA variation. These data, and the ease of use and potential for multiplexing of these markers, suggest that cpSSRs will be of great utility in population genetics, germplasm management, evolutionary and phylogenetic studies as well as in, the analysis of material from introgression and somatic-fusion experiments. Interestingly, the polymorphism arising from one of the more-polymorphic chloroplast loci examined, does not originate solely from the SSR, and is due to variation in the copy number of two tandemly arrayed sequence elements. Received: 15 December 1998 / Accepted: 9 February 1999     

Molecular phytogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes

We investigated the molecular phylogeny of conifers using restriction endonuclease fragment length polymorphism of six polymerase chain reaction-amplified chloroplast genes — frxC, rbcL, psbA, psbD, trnK, and 16S. We detected 227 total site changes among species, representing 23, 26, 38, 48, 67, and 25 site changes in frxC, psbA, psbD, rbcL, trnK and 16S, respectively. The mean nucleotide substitution was 10.75% (SD 0.573) among species in five families. Forty maximally parsimonious trees were obtained using the Wagner parsimony method, and a 50% majority-rule consensus tree was obtained from them. Data analysis produced similar basic patterns when both the Wagner parsimony and the neighbor-joining methods were applied, and the main lineages were clearly separated. Taxaceae and Cephalotaxaceae species were used as the out-groups when applying Wagner parsimony methods. With the Wagner method, the consistency index was 0.510, the retention index was 0.879, and tree length was 435 steps. Our results indicated that Cupressaceae and Taxodiaceae are closely related families and that Sciadopitys verticillata is the basal lineage of Cupressaceae and Taxodiaceae. The neighbor-joining tree is similar to the 50% majority-rule consensus of the 40 Wagner parsimony trees except for the position of Keteleeria daversifolia, the Picea and Cedrus group, and the divergence within Cupressaceae.     

Long inverted repeats in eukaryotic genomes: recombinogenic motifs determine genomic plasticity

Inverted repeats are unstable motifs in a genome, having a causal relation to fragment rearrangements and recombination events. We have investigated long inverted repeats (LIR) of > 30 bp in length in eukaryotic genomes to assess their contribution to genome stability. An algorithm was first designed for searching for LIRs with < 2 kb internal spacers and >85% identity (degree of homology between repeat copies of a LIR). There are much fewer LIRs in yeast, fruitfly, pufferfish and chicken than in Caenorhabditis elegans, zebrafish, frog and human. However, the high LIR frequencies do not necessarily imply high genome instability because of variant internal spacers and stem lengths and identities. From the collection of identified LIRs, we selected recombinogenic LIRs that had a short internal spacer and a high copy identity and were prone to induce high instability. We found that a relatively high proportion (5-9.8%) of the LIRs in C. elegans, zebrafish and frog were recombinogenic LIRs. In contrast, the proportions in human and mouse LIRs were quite low (0.4-1.1%) basically accounting for long internal spacers. We suggest that C. elegans, zebrafish and frog genomes are unstable in terms of the LIR frequency and the proportion of recombinogenic LIRs. For the other genomes, LIRs most likely have a minor impact.     

A chloroplast DNA hypervariable region in eucalypts

Eucalypt chloroplast DNA (cpDNA) provides useful markers for phylogenetic and population research including gene flow and maternity studies. All cpDNA studies in Eucalyptus to date have been based on the RFLP technique, which requires relatively large amounts of clean DNA. The objective of this study was to develop PCR-based cpDNA markers for Eucalyptus. The chloroplast genome of Eucalyptus, like that of most angiosperms, possesses inverted repeats (IR). The two junctions between the IRs and the large single copy (LSC) regions are defined as J_LA andJ_LB. The region surrounding the J_LA junction was sequenced from 26 Eucalyptus DNA samples (21 of E. globulus, plus 5 other species), andtheJ_LB region was sequenced using 5 of these samples. The samples were chosen to represent all major haplotypes identified in previous cpDNA RFLP studies. The J_LA products were 150–210 bp in size, while those fromJ_LB were approximately 500 bp in size. Eighteen mutations were scored in total. Extensive variation was found in the IR within the intergenic spacer between rpl2 and the IR/LSC junctions. Many of these characters were complex indels. One sample of E. globulus possessed a relatively large (38 bp) insertion which caused displacement of the IR/LSC junctions. This is the first report of intraspecific variation in the position of IR/LSC junctions; interspecific variation was also found. The LSC region near J_LB had a low rate of mutation and none were informative. The LSC region near J_LA possessed 2 informative mutations. The variation revealed from these sequences reflects the differentiation previously uncovered in an extensive RLFP analysis on the same samples. These results suggest that the J_LA region will provide very useful cpDNA polymorphisms for future studies in Eucalyptus. Received: 20 March 1999 / Accepted: 16 December 1999     

Achlya mitochondrial DNA: gene localization and analysis of inverted repeats

Summary Mitochondrial DNA from four strains of the oomycete Achlya has been compared and nine gene loci mapped, including that of the ribosomal protein gene, var1. Examination of the restriction enzyme site maps showed the presence of four insertions relative to a map common to all four strains. All the insertions were found in close proximity to genic regions. The four strains also cotained the inverted repeat first observed in A. ambisexualis (Hudspeth et al. 1983), allowing an examination by analysis of retained restriction sites of the evolutionary stability of repeated DNA sequences relative to single copy sequences. Although the inverted repeat is significantly more stable than single copy sequences, more detailed analysis indicated that this stability is limited to the portion encoding the ribosomal RNA genes. Thus, the apparent evolutionary stability of the repeat does not appear to derive from the inverted repeat structure per se.Abbreviations ATPase 6, 9 genes for ATPase subunits 6 and 9 - COI, II, III genes for cytochrome oxidase subunits 1, 2, and 3 - COB gene for apocytochrome b - L-, S-RNA genes for the mitochondrial large and small ribosomal RNAs - mtDNA mitochondrial DNA - var1 gene for the S. cerevisiae mitochondrially, encoded ribosomal protein - m.u. map units - bp base pairs - kb kilobase pairs     

The first report describes features of the chloroplast genome of Withania frutescens

Genomic studies not only help researcher not only to identify genomic features in organisms, but also facilitate understanding of evolutionary relationships. Species in the Withania genus have medicinal benefits, and one of them is Withania frutescens, which is used to treat various diseases. This report investigates the nucleotides and genic features of chloroplast genome of Withania frutescens and trying to clarify the evolutionary relationship with Withania sp and family Solanaceae. We found that the total size of Withania frutescens chloroplast genome was 153.771 kb (the smallest chloroplast genome in genus Withania). A large single-copy region (91.285 kb), a small single-copy region (18.373 kb) form the genomic region, and are distinct from each other by a large inverted repeat (22.056 kb). 137 chloroplast genes are found including 4 rRNAs, 38 tRNAs and 83 protein-coding genes. The Withania frutescens chloroplast genome as well as four closest relatives was compared for features such as structure, nucleotide composition, simple sequence repeats (SSRs) and codon bias. Compared to other Withania species, Withania frutescens has unique characteristics. It has the smallest chloroplast genome of any Withania species, isoleucine is the major amino acid, and tryptophan is the minor, In addition, there are no ycf3 and ycf4 genes, fourth, there are only fifteen replicative genes, while in most other species there are more. Using fast minimum evolution and neighbor joining, we have reconstructed the trees to confirm the relationship with other Solanacaea species. The Withania frutescens chloroplast genome is submitted under accession no. ON153173.     

Gene localization on the chloroplast DNA of the maiden hair fern;Adiantum capillus-veneris

Gene maps were constructed for the inverted repeat region and for the adjacent large single copy region of the chloroplast genome of the maiden hair fern,Adiantum capillus-veneris L. Gene order and organization was very different from the typical angiosperm chloroplast genome (e.g. tobacco). Elongation of inverted repeat and a minimum of two inversions must be postulated to account for the unusual genome structure.     

Recombination between chloroplast genomes of Trachystoma ballii and Brassica juncea following protoplast fusion

We document here the presence of a recombinant plastome in a cytoplasmic male sterile (CMS) line of Brassica juncea developed from the somatic hybrid Trachystoma ballii + B. juncea. Restriction endonuclease digestion of the chloroplast (cp) DNA has revealed that the recombinant plastome gives rise to novel fragments in addition to the parent-specific fragments. Analysis of the 16S rRNA region by Southern hybridization shows no variation between B. juncea, T. ballii and the CMS line. The rbcL gene region of the recombinant plastome is identical to that in T. ballii. Analysis with probes for psbA and psbD using single and double DNA digests indicates that the hybridization patterns of the recombinant plastome are identical to those of the parents in digests obtained with some restriction enzymes, while novel bands hybridize to probes in other digests. In the psbA region, a B. juncea-specific PstI site and a T. ballii-specific EcoRI site are found in the recombinant plastome. The psbD region of the recombinant plastome contains a B. juncea-specific HindIII site and T. ballii-specific BamHI and HpaII sites. These results indicate the occurrence of intergenomic recombination between the chloroplasts of T. ballii and B. juncea in the somatic hybrid from which the CMS line was developed. The recombined plastome appears to be a mosaic of fragments specific to both parents and the recombination event has occurred in the single-copy regions. These recombinational events have not caused any imbalance in the recombinant plastome in terms of chloroplast-related functions, which have remained stable over generations. Received: 3 March 1998 / Accepted: 5 August 1998     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

The contribution of short repeats of low sequence complexity to large conifer genomes

The abundance and genomic organization of six simple sequence repeats, consisting of di-, tri-, and tetranucleotide sequence motifs, and a minisatellite repeat have been analyzed in different gymnosperms by Southern hybridization. Within the gymnosperm genomes investigated, the abundance and genomic organization of micro- and minisatellite repeats largely follows taxonomic groupings. We found that only particular simple sequence repeat motifs are amplified in gymnosperm genomes, while others such as (CAC)₅ and (GACA)₄ are present in only low copy numbers. The variation in abundance of simple sequence motifs reflects a similar situation to that found in angiosperms. Species of the two- and three-needle pine section Pinus are relatively conserved and can be distinguished from Pinus strobus which belongs to the five-needle pine section Strobus. The hybridization pattern of Picea species, bald cypress and gingko were different from the patterns detected in the Pinus species. Furthermore, sequences with homology to the plant telomeric repeat (TTTAGGG)_n have been analyzed in the same set of gymnosperms. Telomere-like repeats are highly amplified within two- and three- needle pine genomes, such as slash pine (Pinus elliottii Engelm. var. elliottii), compared to P. strobus, Picea species, bald cypress and gingko. P. elliottii var. elliottii was used as a representative species to investigate the chromosomal organization of telomere-like sequences by fluorescence in situ hybridization (FISH). The telomere-like sequences are not restricted to the ends of chromosomes; they form large intercalary and pericentric blocks showing that they are a repeated component of the slash pine genome.Conifers have genomes larger than 20000 Mbp, and our results clearly demonstrate that repeats of low sequence complexity, such to (CA)₈, (GA)₈, (GGAT)₄ and (GATA)₄, and minisatellite- and telomere-like sequences represent a large fraction of the repetitive DNA of these species. The striking differences in abundance and genome organization of the various repeat motifs suggest that these repetitive sequences evolved differently in the gymnosperm genomes investigated. Received: 1 October 1999 / Accepted: 3 November 1999     

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

Previous studies have estimated that, in angiosperms, the synonymous substitution rate of chloroplast genes is three times higher than that of mitochondrial genes and that of nuclear genes is twelve times higher than that of mitochondrial genes. Here we used 12 genes in 27 seed plant species to investigate whether these relative rates of substitutions are common to diverse seed plant groups. We find that the overall relative rate of synonymous substitutions of mitochondrial, chloroplast and nuclear genes of all seed plants is 1:3:10, that these ratios are 1:2:4 in gymnosperms but 1:3:16 in angiosperms and that they go up to 1:3:20 in basal angiosperms. Our results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant groups and that gymnosperms have smaller ratios than angiosperms.     

Survey of simple sequence repeats in completed fungal genomes

The use of simple sequence repeats or microsatellites as genetic markers has become very popular because of their abundance and length variation between different individuals. SSRs are tandem repeat units of 1 to 6 base pairs that are found abundantly in many prokaryotic and eukaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced fungal genomes. We analyzed and compared the occurrences, relative abundance, relative density, most common, and longest SSRs in nine taxonomically different fungal species: Aspergillus nidulans, Cryptococcus neoformans, Encephalitozoon cuniculi, Fusarium graminearum, Magnaporthe grisea, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Ustilago maydis. Our analysis revealed that, in all of the genomes studied, the occurrence, abundance, and relative density of SSRs varied and was not influenced by the genome sizes. No correlation between relative abundance and the genome sizes was observed, but it was shown that N. crassa, the largest genome analyzed had the highest relative abundance of SSRs. In most genomes, mononucleotide, dinucleotide, and trinucleotide repeats were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. Our analysis showed that the relative abundance of SSRs in fungi is low compared with the human genome and that longer SSRs in fungi are rare. In addition to providing new information concerning the abundance of SSRs for each of these fungi, the results provide a general source of molecular markers that could be useful for a variety of applications such as population genetics and strain identification of fungal organisms.     

Homologues of the green algal gidA gene and the liverwort frxC gene are present on the chloroplast genomes of conifers

Strong hybridization signals were obtained from total DNA of two conifers, lodgepole pine (Pinus contorta) and Norway spruce (Picea abies), in a Southern blot analysis using a probe derived from the chloroplast gidA gene of the green alga Chlamydomonas reinhardtii. The pine fragments detected by the probe were found to originate from the chloroplast genome and, as judged by the signal intensity, this was also true for the spruce fragments. Sequence analysis of the hybridizing pine chloroplast DNA region revealed an open reading frame potentially encoding a 459 amino acid polypeptide, highly homologous to that deduced from the algal gene and to ORF465 of liverwort chloroplast DNA. Upstream of the gidA sequence, we found a trnN(GUU) gene and an open reading frame of 291 codons which was 78% identical to the frxC gene of liverwort. Since ORF465 is located immediately downstream of trnN and frxC in liverwort, the genetic organization of this region is very similar in the two plants. In contrast, neither the gidA nor the frxC gene is present in the chloroplast DNA of tobacco or rice. It was recently reported that deletions in the gidA region of the chloroplast genome of Chlamydomonas reinhardtii abolish the light-independent pathway of chlorophyll synthesis which exists in many algae and lower plants. The presence of the gidA gene on the chloroplast genomes of conifers may therefore be of significance with respect to the ability of these plants to synthesize chlorophyll in the dark.     

A Petunia hybrida chloroplast DNA region, close to one of the inverted repeats, shows sequence homology with the Euglena gracilis chloroplast DNA region that carries the putative replication origin

Summary Three distinct chloroplast (cp) DNA fragments from Petunia hybrida, which promote autonomous replication in yeast, were mapped on the chloroplast genome. Sequence analysis revealed that these fragments (called ARS A, B and C) have a high AT content, numerous short direct and inverted repeats and at least one yeast ARS consensus sequence 5A/TTTTATPuTTTA/T, essential for yeast ARS activity. ARS A and B also showed the presence of (semi-)conserved sequences, present in all Chlamydomanas reinhardii cpDNA regions that promote autonomous replication in yeast (ARS sequences) or in C. reinhardii (ARC sequences). A 431 bp BamHI/EcoRI fragment, close to one of the inverted repeats and adjacent to the ARS B subfragment contains an AT-rich stretch of about 100 nucleotides that show extensive homology with an Euglena gracilis cpDNA fragment which is part of the replication origin region. This conserved region contains direct and inverted repeats, stem-and-loop structures can be folded and it contains an ARS consensus sequence. In the near vicinity a GC-rich block is present. All these features make this cpDNA region the best candidate for being the origin of replication of P. hybrida cpDNA.     

Associations between inverted repeats and the structural evolution of bacterial genomes

The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.