Chloroplast Non-coding Regions Research Articles

Phylogeography of Arabis serrata (Brassicaceae) in the Japanese Archipelago based on chloroplast DNA variations

AbstractArabis serrata (Brassicaceae), a perennial plant widely distributed along the Japanese Archipelago, occurs in various habitats: for example, limestone zones, serpentine barrens, volcanic soils, and roadsides. It likely survived by adapting to its surrounding environment, resulting in great morphological and ecological variation. In this study, we performed a phylogeographic analysis to examine past changes in the distribution of A. serrata following climate oscillations during the Pleistocene. To cover most of A. serrata's range, leaves were collected from eight to ten individuals randomly selected from each of 37 populations in the Japanese Archipelago. Two chloroplast noncoding regions of the samples were amplified and sequenced: trnT(GGU)‐psbD and trnH(GUG)‐psbA spacers. Twenty‐five haplotypes were detected and distinguished by 31 substitutions. Four main haplotypes were observed in many populations distributed throughout the Japanese Archipelago. According to the genetic boundaries detected using the Monmonier algorithm, A. serrata is clustered into four groups, each including several populations: Hokkaido Island, northern mainland Honshu, central Japan, and western Japan. The boundaries, however, were not robust because all genetic parameters did not support the differentiation among groups. These results indicate the absence of an obvious geographic structure in the distribution of A. serrata, suggesting that this species has experienced a rapid range expansion in postglacial times.

A new wild type of Citron (Citrus medica L., Rutaceae) identified through morphology and psbM-trnD spacer region of chloroplast DNA

This study showed that Themachhi is genetically very close to C. medica and consistently grouped with the typical citron in all the phylogenetic trees; hence revealed the identity of ‘Themachhi’ as a natural wild type of C. medica. Taxonomic identity and well-supported phylogenetic relationships of doubtful and taxonomically uncertain taxa are highly requisite for developing crop improvement programmes and suitable conservation strategies. In Citrus, several natural varieties and hybrids of ambiguous origin have been existing due to several factors such as frequent intergeneric and interspecific hybridization, apomixis, bud mutations, polyploidy and diverse eco-geographical distribution. In Northeast India, an important unidentified type of Citrus, i.e. ‘Themachhi’ is found naturally in Garo Hills, Meghalaya, which is morphologically very close to C. medica and C. limon. The sequences of chloroplast non-coding region psbM-trnD of 16 accessions of Citrus were utilized to confirm the taxonomic identity of ‘Themachhi’ and also to infer its phylogenetic affinities to related taxa. The nucleotide frequencies were 32.86 % for A and T and 17.4 % for C and G. Pairwise genetic divergence between the accessions of Citrus ranged from 0.002 to 0.036 with an average of 0.017. ‘Themachhi’ showed least genetic divergence with C. medica (0.013) and highest divergence with C. limon (average 0.024). All the accessions of Citrus were grouped into three main clusters (C. medica, C. reticulata and C. maxima clusters) in both the MP and ML trees with high bootstrap value (>60 %). In the MP and ML trees, both accessions of ‘Themachhi’ were closely attached with C. medica cluster with high bootstrap value (98 %). Close genetic affinity and consistently grouping of “Themachhi” with typical citron (C. medica) in both the phylogenetic trees revealed the identity of ‘Themachhi’ as a natural wild type of C. medica.

Molecular polymorphism and phylogenetic relationships within Tunisian date palm (Phoenix dactylifera L.): Evidence of non-coding trnL-trnF regions of chloroplast DNAs

Phoenix dactylifera L. were analyzed for DNA sequence diversity in the non-coding region of chloroplast DNA. The trnL-trnF intergenic spacer sequences were used as genetic markers to establish refined genetic relationships for differentiating date-palm accessions collected from Tunisian oasis. A single DNA band of approximately 400bp was amplified from each Tunisian date-palm cultivars. Using the Kimura-2 method, nucleotide sequences were aligned using the MEGA 5.2 program to calculate pairwise divergence of trnL-trnF spacer sequences between cultivars. The relatively high AT values (60.5–67.6%) of trnL-trnF intergenic spacer may explain the high proportion of the identified transversions (ti/tv=0.67). These results suggest the rate of nucleotide diversity with a great variation level of chloroplast non-coding region. The analyzed data illustrated a considerable level of variability in the genetic pool of the local germplasm. In fact, relationships inferred from the cpDNA analysis suggest several clades, which do not show geographical correspondence. In the other hand, 14 haplotypes were detected among 31 individuals examined, yielding a haplotype diversity of 0.854 and a level of nucleotide diversity of (0.0081). Selective neutrality tests show that Tajima's as well as Fu and Li's tests were negative and not significant in the studied cultivars. The cytoplasm variability indicates a narrow genetic base within date-palm cultivars. The opportunity of the designed methods is discussed with the molecular characterization of genotypes in order to enhance the conservation and the improvement of the local date-palm germplasm.

Chloroplast DNA analysis in Tunisian date-palm cultivars (Phoenix dactylifera L.): Sequence variations and molecular evolution of trnL (UAA) intron and trnL (UAA) trnF (GAA) intergenic spacer

Sequences of trnL intron and trnL–trnF spacer of chloroplast DNA of date palm (Phoenix dactylifera L.) were analyzed to detect polymorphism and elucidate molecular evolution. The size of these non-coding regions ranged from 364 to 397 for the intergenic spacer, from 545 to 591 for the intron and from 897 to 981 base pairs for the combined sequences. The averages of GC-contents were 33.3%, 35.9% and 34.8% in the spacer, the intron and the combined data, respectively. The overall ration of transition/transversion R was of 2.19 for the intergenic spacer, indicating that transitions are more frequent than transversions. Haplotypic and nucleotide diversities showed high level of variation of chloroplast non-coding regions. Phylogenetic trees generated using neighbor joining and maximum parsimony analyses showed two groups. The structure of which is independent of the geographic origin or sex of trees. The observed mismatch distribution of pairwise nucleotide differences for cpDNA differed from the one predicted under a model of expansion, as the shapes of the functions was not unimodal. This deviation was also supported by tests of neutrality, which showed that Tajima's D and Fu's Fs values were mostly negative but always insignificant. These results rejected the hypothesis that there has been recent demographic population growth in this species. We may conclude that date palm chloroplast genome provides a new efficient opportunity to evaluate the genetic diversity and to examine the phylogenetic relationships in this crop.

Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners

Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity. • We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila, S. alabamensis, and S. jonesii. The same microsatellite loci were used to examine a single field site of three more widespread species (S. alata, S. leucophylla, and S. rubra subsp. wherryi). • All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila. • The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical.

Chloroplast DNA Intraspecific Phylogeography of Prairie Cordgrass (Spartina pectinata Bosc ex Link)

Chloroplast DNA (cpDNA) sequences are appropriate for studying intraspecific phylogeography. Comparing cpDNA phylogeny with different cytotypes provides insights into the origin and establishment of polyploid species. We have previously defined the geographic distribution of cytotypes in prairie cordgrass throughout the different regions of the United States. In this study, chloroplast haplotype variation is explored in 54 populations of prairie cordgrass, using nine noncoding chloroplast regions. These chloroplast analyses were combined with the cytotype surveys of prairie cordgrass to infer the phylogeography and to elucidate the origin of the different cytotypes. In this study, we identified three haplotypes, Prairie Cordgrass Group 1 (PCG1), Prairie Cordgrass Group 2 (PCG2), and Prairie Cordgrass Group 3 (PCG3). In general, related haplotypes were strongly associated with geographic distribution. Useful insertions–deletions (indels) were also found among prairie cordgrass populations. The PCG1 haplotypes collected inthe East North Central to the New England regions of the US, were polyploid (tetraploid, hexaploid, and octoploids), while the PCG2 haplotypes, found in southern South Dakota, Iowa, and Missouri, were primarily octoploids, but also included a small number of tetraploids. The PCG3 haplotypes were octoploids and were collected in North Dakota, South Dakota, and Minnesota.

Colour polymorphism in common primrose (Primula vulgaris Huds.): many colours–many species?

Primula vulgaris exhibits flower colour polymorphism in the eastern part of its range, especially pronounced on the NE coast of the Black Sea. This polymorphism in the Caucasian populations has been taxonomically described and some segregated species are listed as rare and endangered. We used sequence variation in two chloroplast noncoding regions (trnL–trnF and rpll32–trnL) and the complete nuclear internal transcribed spacer (ITS) of ribosomal DNA region to investigate correspondence between flower colour and geographical distribution of both nuclear and chloroplast haplotypes. It appears that variability in these DNA regions does not correlate with flower colour, being, however, clearly structured geographically. We used nested clade analysis to explore this geographical structure. It seems that the territory of the Colchis refugium on the E coast of the Black Sea contains both the highest flower colour and haplotype diversities. The results suggest that common primroses colonized the NE coast of the Black Sea from this refugium, spreading along the coast westward. At the same time, the analysis of ITS haplotypes indicates that P. vulgaris colonized the Crimea from NW Anatolia. This makes it clear that no segregated species can be recognized within flower colour polymorphic P. vulgaris in the Caucasus region. However, its phylogeography needs further detailed study on a broader scale.

Application of the phylogenetic informativeness method to chloroplast markers: A test case of closely related species in tribe Hydrangeeae (Hydrangeaceae)

In evolutionary biology appropriate marker selection for the reconstruction of solid phylogenetic hypotheses is fundamental. One of the most challenging tasks addresses the appropriate choice of genomic regions in studies of closely related species. Robust phylogenetic frameworks are central to studies dealing with questions ranging from evolutionary and conservation biology, biogeography to plant breeding. Phylogenetic informativeness profiles provide a quantitative measure of the phylogenetic signal in markers and therefore a method for locus prioritization. The present work profiles phylogenetic informativeness of mostly non-coding chloroplast regions in an angiosperm lineage of closely related species: the popular ornamental tribe Hydrangeeae (Hydrangeaceae, Cornales, Asterids). A recent phylogenetic study denoted a case of resolution contrast between the two strongly supported clades within tribe Hydrangeeae. We evaluate the phylogenetic signal of 13 highly variable plastid markers for estimating relationships within and among the currently recognized monophyletic groups of this tribe. A selection of combined loci based on their phylogenetic informativeness retrieved more robust phylogenetic hypotheses than simply combining individual markers performing best with respect to resolution, nodal support and accuracy or those presenting the highest number of parsimony informative characters. We propose the rpl32–ndhF intergenic spacer (IGS), trnV–ndhC IGS, trnL–rpl32 IGS, psbT–petB region and ndhA intron as the best candidates for future phylogenetic studies in Hydrangeeae and potentially in other Asterids. We also contrasted the phylogenetic informativeness of coded indels against substitutions concluding that, despite their low phylogenetic informativeness, coded indels provide additional phylogenetic signal that is nearly free of noise. Phylogenetic relationships obtained from our total combined analyses showed improved resolution and nodal support with respect to recently published results.

Phylogenetic analysis of Turkish Iris species inferred from non-coding chloroplast region

Phylogenetic analysis of Turkish Iris species inferred from non-coding chloroplast region

Multiple origins of allopolyploid wheatgrass Elymus caninus revealed by RPB2, PepC and TrnD/T genes

We examined evolutionary mechanisms in the tetraploid Elymus caninus by comparing the phylogenetic relationships of 21 accessions suggested by sequence data from two single copy nuclear genes, the largest subunit of RNA polymerase II (RPB2) and phosphoenolpyruvate carboxylase (pepC), and one non-coding chloroplast region, TrnD/T. Elymus caninus is known combining two different genomes, an St genome and an H genome. Data from two single copy nuclear genes showed that there are two versions of the St genome in the species, St1 and St2. Most accessions combined one of these versions with an H genome version but two accessions had both versions of the St sequence for RPB2. This suggests that the RPB2gene may have been duplicated without chromosome doubling, possibly induced by transposable element. Our data also indicate that the H genome sequences in E. caninus have multiple origins, and a close phylogenetic relationship between Hordeum bogdanii and H sequences in some accessions of E. caninus. Thus, it is more likely that H. bogdanii is one of the major donors of the H copy in E. caninus. The maternal origin of E. caninus is the St genome species. There was no correlation between the geographic origin of the accessions and their sequence divergence.

Testing the variability of chloroplast sequences for plant phylogeography

Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.

Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae)

Although there is growing evidence that autopolyploidy is a widespread and important evolutionary phenomenon, it has received less attention than allopolyploidy. Medicago sativa comprises several diploid and autopolyploid taxa, including autotetraploid cultivated alfalfa, and affords an opportunity to elucidate the evolutionary history of a morphologically and genetically complex autopolyploid system. Phylogenies and haplotype networks were constructed from two chloroplast noncoding regions (rpl20-rps12 and trnS-trnG spacers) across seven diploid and polyploid infraspecific taxa of M. sativa and five additional closely related Medicago species, and genetic differentiation was estimated. The two most prominent M. sativa autopolyploids have contrasting evolutionary histories. Chloroplast data support a simple autopolyploid origin of subsp. sativa (alfalfa) from diploid subsp. caerulea, from which it is distinguishable in several quantitative characters. In contrast, morphologically identical diploid and autopolyploid cytotypes of subsp. falcata were found to possess very different chloroplast haplotypes, suggesting past introgression from M. prostrata into the polyploid. Despite the presence of hybrids between tetraploid subspecies falcata and sativa, there was little evidence of introgression of chloroplast genomes from either subspecies into the other. Autopolyploid evolution in M. sativa is complicated and has followed very different paths in different subspecific taxa. The potential exists for gene flow in virtually all combinations of subspecies both within and between ploidies, yet despite the existence of hybrids, morphologically and genetically distinctive subspecies persist.

Phylogeographic studies of Brazilian “campo-rupestre” species: Wunderlichia mirabilis Riedel ex Baker (Asteraceae)

Wunderlichia mirabilis Riedel ex Baker, a Brazilian wind-dispersed tree species, has a disjunct pattern of geographical distribution. This species occurs in ‘campo rupestre’ locations of the Espinhaço Range, andGoiás Mountains, Brazil. The phylogeography of W. mirabilis was reconstructed on the basis of the genetic variability and phylogeny of the nuclear (ITS) and chloroplast (trnL) non-coding spacer regions. AMOVA andMantel analysis revealed for both markers that genetic variability is high within populations and moderate-tohigh among populations. Rates of seed flow are higher than those of pollen flow, and there is a non-significantgenetic x geographic correlation. The spread of Wunderlichia mirabilis probably occurred from Serra do Cabral through other serras in the Espinhaço Range of Minas Gerais and Espírito Santo, in an easterly direction, andthrough Goiás Mountains, Serra da Canastra in Minas Gerais and São Paulo in a westerly movement from the Serra do Cabral, Minas Gerais.

Cyto-nuclear discordance in the genetic relationships among Tunisian fig cultivars ( Ficus carica L.): Evidence from non coding trnL– trnF and ITS regions of chloroplast and ribosomal DNAs

Genetic diversity studies were conducted to evaluate intra-specific relationships in Tunisian fig (Ficus: Moraceae) using sequences of the ITS regions of nuclear ribosomal DNA and the chloroplast non-coding region trnL– trnF ( trnL intron, and trnL [UAA]–exon– trnF [GAA] intergenic spacer). All data sets suggest that the sequences obtained showed variations either on their lengths or on their nucleotide compositions. The mean size of these nuclear and cytoplasmic non-coding regions is 697.5 and 1035 base pairs for ITS and trnL– trnF chloroplast DNA, respectively. Our results suggest that the substitution rate estimated for the ITS sequences of nuclear DNA is greater than the one unregistered for the non-coding regions of chloroplast DNA. Therefore, chloroplast DNA shows more homoplasy than the nuclear ribosomal DNA. In fact, the consistency (CI) and retention (RI) indexes calculated for nuclear and cytoplasmic DNAs show values of 0.420 and 0.490 for chloroplast DNA and 0.573 and 0.387 for ribosomal DNA, respectively. The nuclear DNA has more resolution of genetic relationships between cultivars. In addition, the result suggests that the cultivars studied are clustered independently from their geographical origin and the male trees did not thoroughly diverge from the common figs. The discordance between chloroplast and the nuclear topology is revealed. The lack of congruence between the two data sets may be a result of hybridization or introgression. Our result showed that the nuclear and cytoplasmic sequences are useful for germplasm discrimination as well as for investigation of patterns of variation in fig.

Chloroplast DNA non-coding sequences variation in Aegilops tauschii Coss.: evolutionary history of the species

Sequences of four chloroplast DNA non-coding regions, about 3,000 bp in total, were analysed in 112 Aegilops tauschii accessions, 56 of ssp. tauschii and 56 of ssp. strangulata, representing all of the species range. One inversion, 8 insertions/deletions, 18 base pair substitutions and 5 microsatellite loci were found. The data revealed that Ae. tauschii originated in Caucasia. Neither of the two Ae. tauschii subspecies was an ancestor to one another. Aegilops tauschii divided into ssp. tauschii and ssp. strangulata at the very beginning of its existence as a species. Subspecies tauschii was the first to start geographic expansion and relatively rapidly occupied a vast area from Caucasia—eastward up to central Tien Shan and western Himalayas. In contrast to ssp. tauschii, geographic spread of ssp. strangulata was a complicated, multi-stage and slow process. At the beginning of ssp. strangulata evolutionary history its major phylogenetic lineage for a lengthy time span had existed as a small isolated population. Several forms of ssp. strangulata, better adapted to relatively moister and cooler habitats, had originated. Each of these forms has gradually forced out ssp. tauschii from some part of its area in the west, up to central Kopet-Dag.

Relationships in the Lupinus albifrons Species Complex (Fabaceae) based on Two Highly Variable Chloroplast Regions

Abstract The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular dat...

Evolutionary biogeography of Manihot (Euphorbiaceae), a rapidly radiating Neotropical genus restricted to dry environments

Aim The aims of this study were to reconstruct the phylogeny of Manihot, a Neotropical genus restricted to seasonally dry areas, to yield insight into its biogeographic history, and to identify the closest wild relatives of a widely grown, yet poorly known, crop: cassava (Manihot esculenta). Location Dry and seasonally dry regions of Meso- and South America. Methods We collected 101 samples of Manihot, representing 52 species, mostly from herbaria, and two outgroups (Jatropha gossypiifolia and Cnidoscolus urens). More than half of the currently accepted Manihot species were included in our study; our sampling covered the whole native range of the genus, and most of its phenotypic and ecological variation. We reconstructed phylogenetic relationships among Manihot species using sequences for two nuclear genes and a non-coding chloroplast region. We then reconstructed the history of traits related to growth form, dispersal ecology and regeneration ability. Results Manihot species from Mesoamerica form a grade basal to South American species. The latter species show a strong biogeographic clustering: species from the cerrado form well defined clades, species from the caatinga of north-eastern Brazil form another, and so do species restricted to forest gaps along the rim of the Amazon basin. Vine and tree growth habits evolved repeatedly in the genus, as did fruit indehiscence and loss of ant-mediated seed dispersal. Main conclusions The genus Manihot probably originated in Mesoamerica, where it diversified prior to colonizing South America. Within South America, several groups then radiated southwards and eastwards within all kinds of seasonally dry lowland habitats. Some species also adapted to more humid environments, such as forest gaps, around the rim of the Amazon basin. Given the limited dispersal abilities of Manihot species, we propose that this radiation is most likely to have occurred only after, or shortly before, the completion of the Isthmus of Panama, around 3.5 Ma. Our results are in agreement with the past existence of a corridor of dry vegetation through Amazonia or along the eastern South American coast. In addition, our phylogeny allows identification of cassava’s closest wild relatives.

Molecular phylogeny of Osmanthus (Oleaceae) based on non-coding chloroplast and nuclear ribosomal internal transcribed spacer regions

Abstract The phylogenetic relationships of Osmanthus Lour. were investigated using the nuclear ribosomal internal transcribed spacer (ITS) regions and non-coding chloroplast regions (psbA-trnH, trnL-F). The two datasets support the conclusion that Osmanthus is polyphyletic, with some species of the subtribe Oleinae nested within Osmanthus. Osmanthus didymopetalus P. S. Green is nested within the clade formed by species of section Osmanthus in two trees. Osmanthus attenuatus P. S. Green, O. yunnanensis P. S. Green, and O. gracilinervis R. L. Lu of traditional section Osmanthus are clearly divergent from other accessions, and do not form a monophyletic group with other Osmanthus accessions. Osmanthus marginatus Hemsl. is embedded in the clade formed by species of section Osmanthus in the ITS tree. In cpDNA trees all species of section Osmanthus are placed in the large clade and all species of section Leiolea formed a group. The taxonomic incongruence among trees for ITS and cpDNA indicate hybridization, as introgression may have occurred among some species of sections Osmanthus and Leiolea. Phylogeny of Osmanthus is discussed in light of molecular and morphological data, and a revised infrageneric classification with three sections (Leiolea, Siphosmanthu, and Osmanthus) is presented. The section Linocieroides is abandoned and united with section Osmanthus.

Unraveling Extensive Paraphyly in the Genus <I>Hydrangea</I> s. l. with Implications for the Systematics of Tribe Hydrangeeae

Abstract Several representatives of Hydrangeaceae tribe Hydrangeeae are popular in the horticultural trade for their inflorescences with attractive marginal flowers, resulting in many hybrids and cultivars. However, despite previous morphological and molecular studies, the phylogenetic relationships between the nine currently recognized genera in this clade are still largely unclear, and the widely used infrageneric classification of the genus Hydrangea by McClintock (which was mainly based on the study of herbarium specimens) requires critical reevaluation. We present a partially well resolved and well supported phylogeny of the tribe Hydrangeeae based on maximum parsimony and Bayesian analyses of multiple coding and noncoding chloroplast regions (rps 16-trnK spacer, trnK intron, trnK exon, matK gene and trnK-psbA spacer). All genera, sections and subsections were included making it a representative sampling for the tribe Hydrangeeae. Hydrangea is paraphyletic with respect to the eight other genera of Hy...

Sequence characteristics and divergent evolution of the chloroplastpsbA-trnH noncoding region in gymnosperms

The psbA-trnH intergenic region is among the most variable regions in the gymnosperm chloroplast genome. It is proposed as suitable for DNA barcoding studies and is useful in phylogenetics at the species level. This region consists of two parts differing in their evolutionary characteristics: 1) the psbA 3’UTR (untranslated region) and 2) the psbA-trnH intergenic spacer. We compared the sequence and RNA secondary structure of the psbA 3’ UTR across gymnosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TGGATTGTTATGT box. The psbA-trnH spacer is highly variable in length and composition. Tandem repeats that form stem-loop structures were detected in both the psbA 3’ UTR and the psbA-trnH spacer. The presence of promoters and stem-loop structures in the psbA-trnH spacer and high sequence variation in this region suggest that psbA and trnH in some gymnosperms are independently transcribed. A comparison of chloroplast UTRs across gymnosperms offer clues to the identity of putative regulatory elements and information on selective constraints imposed on the chloroplast non-coding regions. The present study should inspire researchers to explore the full potential of the psbA-trnH non-coding sequence and to further stimulate its application in a broader spectrum of studies, not limited to phylogenetics and DNA barcoding.