Regions Of Chloroplast Genome Research Articles

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL

Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB – rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB – rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB – rbcL sequences.

Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum).

Polymerase chain reaction and different barcoding methods commonly used for plant identification from metagenomics samples are based on the amplification of a limited number of pre-selected barcoding regions. These methods are often inapplicable due to DNA degradation, low amplification success or low species discriminative power of selected genomic regions. Here we introduce a method for the rapid identification of plant taxon-specific k-mers, that is applicable for the fast detection of plant taxa directly from raw sequencing reads without aligning, mapping or assembling the reads. We identified more than 800 Solanum lycopersicum specific k-mers (32 nucleotides in length) from 42 different chloroplast genome regions using the developed method. We demonstrated that identified k-mers are also detectable in whole genome sequencing raw reads from S. lycopersicum. Also, we demonstrated the usability of taxon-specific k-mers in artificial mixtures of sequences from closely related species. Developed method offers a novel strategy for fast identification of taxon-specific genome regions and offers new perspectives for detection of plant taxa directly from sequencing raw reads.

北海道と宮城県に生育するホトケノザの葉緑体ゲノム trn L (UAA) intron 領域の比較

北海道と宮城県に生育するホトケノザの葉緑体ゲノム trn L (UAA) intron 領域の比較

A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically Important Brassica Species Comprising the Triangle of U.

The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions. Here, we successfully de novo assembled 60 complete chloroplast genomes of Brassica genotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of different Brassica species was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated the Brassica genus into four clades. B. carinata and B. juncea share their chloroplast genome with one of their hybridization donors B. nigra and B. rapa, respectively, which fits the U model. B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions. B. napus clearly has evidence for two independent hybridization events, as it contains either B. rapa chloroplast genomes. The divergence estimation suggests that B. nigra and B. carinata diverged from the main Brassica clade 13.7 million years ago (Mya), while B. rapa and B. oleracea diverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic relationships within the Brassica genus.

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus).

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

Distinctive Architecture of the Chloroplast Genome in the Chlorodendrophycean Green Algae Scherffelia dubia and Tetraselmis sp. CCMP 881.

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.

Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants

Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distributionof SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2)=0.5, P<0.05) and relative abundance (R (2)=0.6, P<0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.

Chloroplast DNA analysis of Tunisian pistachio (Pistacia vera L.): Sequence variations of the intron trnL (UAA)

The trnL (UAA) intron sequences of Pistacia vera ecotypes were employed to reconstruct the phylogeny and to elucidate molecular evolution. A single band of approximately 500pb length was amplified from each cultivars. Nucleotides sequences were aligned using the ClustalW package in the Bioedit program and analyzed with MEGA program version 4. The average of GC content was 35.8% to 39.6%. High values of A+T contents were detected in data sets and may explain the high proportions of transitions founded. Sequence alignment revealed the existence of 50 informative sites and 25 different haplotypes among the 39 cultivars studied yielding to a haplotype diversity of 0.8758 and a level of nucleotide diversity of 0.018. Furthermore, an average value of pairwise nucleotide of 8.641 differences was found, showing a relatively high diversity in the chloroplast intron. The neighbor joining dendrogram shows the presence of fairly high chloroplasts diversity, structured independently from the plant's sex but structured according to geographical origin. The trnL intron mismatch distribution is multimodal; characteristic of a stable population. This was also supported by non-significant values of all neutrality test parameters (Tajima's D and Fu and Li's). Although, the level of apparent diversity is considerable, we may conclude that non-coding regions of chloroplast genome provide a new and practical opportunity to evaluate genetic diversity and to discriminate pistachio cultivars. Revealed cytoplasmic DNA markers are reliable to elaborate a molecular data base to conduct management and breeding programs on local pistachio germplasm.

SPECIES IDENTIFICATION AND DIVERSITY IN FRAGARIA L. USING NUCLEAR REGIONS AND UNIVERSAL CHLOROPLAST SSRS

The US National Fragaria collection at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR) is dynamic through the discovery and collection of new acquisitions and new characteristics that delineate existing species. Previous research using standard Fragaria chloroplast genome regions exhibited limited variation and was unsuccessful at distinguishing between species. The objective of this study was to examine universal chloroplast simple sequence repeats SSRs (cpSSRs) to evaluate diversity in Fragaria species. Four universal cpSSRs (ccmp2, ccmp5, ccmp6, and ccmp7) generated 28 Fragaria haplotypes in ninety four accessions representing 20 Fragaria taxa. Taxa-specific haplotypes were identified for F. nipponica, F. orientalis, F. iinumae and F. nilgerrensis. An octoploid-specific haplotype was observed in cultivated F. x ananassa, F. chiloensis and F. virginiana supporting their close relationship. Genetic diversity using only four universal SSR markers was moderate (0.54, on average) despite the observed homoplasy. Species-specific dehydroascorbate reductase (DHAR) and granule-bound starch synthase (GBSSI-2) gene sequences were also evaluated to identify diploid strawberry species. Marker results and future needs for additional Fragaria-specific primers that may more accurately identify the chloroplast diversity in Fragaria will be discussed.

Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.

The evolutionary divergence of Pinus nigra subsp. pallasiana and its varieties based on noncoding trn regions of chloroplast genome

The Anatolian black pine [Pinus nigra Arnold subsp. pallasiana (Lamb.) Holmboe var. pallasiana] is one of the subspecies of European black pine, growing naturally as a widespread mid-elevation species in the southern, western, and northern Anatolian Mountains of Turkey. Three well-recognized varieties [var. pallasiana, var. fastigiata Businsky with pyramidal form, and var. seneriana (Saatçioğlu) Yalt. with globular-shaped crown with multiple stems] occur naturally, but the studies on them are very limited. These 3 varieties of Anatolian black pine were sampled in natural stands where they coexist to determine evolutionary divergence in the species as well as its evolutionary relationships with other related pine species. A total of 71 trees were sampled to assess molecular divergence patterns in the species by using 3 noncoding trn regions (trnL, trnL-F, and trnV) of chloroplast DNA. The results indicated that trnL and trnV regions were conserved among Anatolian black pine taxa, but the trnL-F region revealed 3 parsimony-informative sites. The sequence diversity in the trnL-F region was useful to separate both var. seneriana and var. fastigiata from Anatolian black pine as well as this species from the other members of section Pinus L. The genetic divergence between 2 varieties (0.0018-0.0027) was greater than the divergence between varieties and Anatolian black pine (0.0009-0.0018). The nucleotide sequences of trn regions obtained from seed megagametophytes of both Anatolian black pine and var. seneriana stands from the same location did not show any divergence, while the trn sequences from needle tissues of var. seneriana diverged from the trn sequences of Anatolian black pine. This divergence suggests that var. seneriana may have evolved as a result of a point mutation in a gene with pleiotropic effects involved in apical dominancy of Anatolian black pine, but this has to be explored further with future studies.

Indigenous genetic lineages of Fagus crenata found in the Izu Peninsula suggest that there was one of refugia for the species during the last glacial maximum

Regions believed to be refugia are known to have lineages indigenous to the regions. The Izu Peninsula, where genus Fagus existed during the last glacial period, was focused on to survey chloroplast DNA of Japanese beech (Fagus crenata Blume) that grew there. DNA sequence analysis of chloroplast genome regions of about 14 kb revealed two new haplotypes, O and E-1, in F. crenata populations in the Izu Peninsula and adjacent regions. Both haplotypes were conceivably derived from haplotype E. The result of the genetic analysis in this study in combination with the result of pollen analyses performed in the past clearly showed that refugia for F. crenata existed in the Izu Peninsula, and that F. crenata now in growth are lineages indigenous to the region.

PCR–RFLP to distinguish three Phyllanthus sp., commonly used in herbal medicines

The herbs Phyllanthus amarus, P. fraternus and P. urinaria, are known for their use in preparation of herbal medicines. These herbs grow together and are morphologically indistinguishable. Hence, collections of these herbs for raw drug trade, frequently contain mixture of the three species. Such mixing can result in preparation of herbal drugs with altered efficacy. To prevent this, it is essential to develop reliable methods/markers for accurate identification of species. Keeping this in view, PCR–RFLP (Polymerase Chain Reaction–Restriction Fragment Length Polymorphism) of chloroplast genome regions was carried out, using six pairs of universal primers of chloroplast DNA for amplification, followed by restriction with HinfI and TaqI in P. amarus, P. fraternus and P. urinaria. Distinct restriction patterns for the three species were obtained in all primer pair-restriction enzyme combinations. Since the primers used are conserved over a wide range of plant taxa, PCR–RFLP technique using universal cpDNA primers may be applied to other medicinal/economically important plants, posed with similar problems of identification.

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

BackgroundCymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution.ResultsThe complete nucleotide sequences of eight individuals from a total of five Cymbidium species’ chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae.ConclusionsPhylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.

Exploring the utility of three nuclear regions to reconstruct reticulate evolution in the fern genus Asplenium

AbstractThree nuclear regions nuclear ribosomal internal transcribed spacer (nrITS) and intron regions of two nuclear low‐copy genes—gapCp, and pgiC, in combination with one chloroplast genome region were employed to explore patterns of reticulate evolution in the fern genus Asplenium. This is the one of the first studies using DNA sequences of multiple nuclear markers in ferns. All three nuclear markers amplified well with PCR and several copies were recovered by cloning PCR products. All three nuclear regions showed congruent results by recovering the neo‐allotetraploid Asplenium adulterinum as the hybrid of diploid A. trichomanes and diploid A. viride. Conflicting results were obtained for several nodes. First, gapCp did not discriminate between A. aethiopicum and A. praegracile whereas the other markers recovered these two taxa as distinct. Conflicts among gene‐trees were found in respect to A. monanthes, chloroplast and pgiC suggested a sister relationship of A. monanthes and A. trichomanes but gapCp and nrITS nested A. monanthes within A. normale. Our results confirm: (i) the usefulness of several nuclear regions, in particular gapCp and pgiC, to unravel reticulate evolution in ferns and species differentiation and (ii) highlights the need to employ more than one nuclear region to obtain reliable hypotheses on reticulate events versus incomplete lineage sorting. Especially, if one assumes that the reticulation event might have occurred in the more distant past. Considering the expected high frequency of reticulate evolution in ferns, the establishment of robust and informative nuclear genomic markers is critical to achieve further progress in our efforts to elucidate fern evolution.

Revealing genetic diversity of tree peonies at micro-evolution level with hyper-variable chloroplast markers and floral traits

Highly variable regions of chloroplast genome were found to be useful in the detection of plant genetic diversity at micro-evolution level. Our methodology will improve understanding and conservation of plant diversity. Tree peonies are famous flowers with about 2,000 cultivars in the world, belonging to Paeonia sect. Moutan of the Paeoniaceae. They are traditionally classified based on flower forms and colors. Due to the limited number of DNA and morphological markers, and the existence of synonyms and homonyms, evaluation on genetic diversity of so many cultivars remains a challenge. In most cases, it is difficult and even impossible to discriminate tree peony cultivars when they are not in flower. In this study, single nucleotide polymorphism detected from the hyper-variable regions of chloroplast genome was employed to separate tree peony cultivars into different maternal lineages which can be expressed briefly by a nucleotide molecular formula. Our approach enabled a much higher resolution of cultivar identification and classification that has not been obtained before. The newly developed hyper-variable chloroplast markers, as an independent source of taxonomic characteristics, provided novel evidences and higher resolution ability that are helpful in building an effective classification system for evaluation, conservation, and utilization of the tree peony germplasm resources at cultivar level.

Structural changes in chloroplast genome accompanying albinism in anther culture of wheat and triticale

The occurrence frequency of structural changes in plastid genome of albino plants from 27 genotypes of Triticum aestivum L. and × Triticosecale Witt. produced by anther culture method was studied. PCR analysis of genome rearrangements in plastids of albino plants has revealed similarity of plasmon changes in the given cereal crops and shown that a number of genes related to photosynthesis exposed to changes in plastid genomes studied. atpB gene, encoding β-subunit of CF1-complex of ATP synthase, was not detected with a high frequency in chlorophyll-deficient plants of wheat and triticale. It is supposed that deletions of photosynthetic genes, especially atpB gene, which take place in evolutionary unstable regions of chloroplast genome with a high frequency, are the major cause of albino plants formation in anther culture of cereals. Genes psbA, psbC, psbD of the photosystem II are amplified practically in all the studied plants of wheat and triticale that verifies the earlier obtained information about conservation of the region including the given genes within the limits of a large singlecopy region of chloroplast DNA.

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0–17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25–1.75): 15.77 (7.48–114.09): 74.79 (36.27–534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383–0.856×10−8 for synonymous substitutions per site per year and 0.036–0.081×10−9 for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.

Chloroplast DNA Diversity of Oak Species in Eastern Romania

The chloroplast DNA of 34 sessile oak (Quercus petraea) and 27 pedunculate oak (Q. robur) populations covering the entire natural distribution of the two oak species in Eastern Romania was investigated using four large regions of the chloroplast genome by PCR and RFLP technique. A total of seven chloroplast DNA haplotypes sensu lato have been observed by analysing 305 mature trees. However, due to the high resolution of the electrophoresis method a total of 22 chloroplast variants could have been detected, with new mutations and fragment combinations in two of the amplified regions: psbC/trnD and trnT/trnF. All of the haplotypes belong to the phylogenetic lineages A and E, which originate from the Balkan Peninsula. Most of genetic diversity is distributed among populations (GST=0.779). The chloroplast DNA haplotypes are shared by the two oak species. Different dispersal abilities may explain the higher value of genetic differentiation among populations in sessile oak than in pedunculate oak.