Association between chloroplast DNA and mitochondrial DNA haplotypes in Prunus spinosa L. (Rosaceae) populations across Europe

Chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) were studied in 24 populations of Prunus spinosa sampled across Europe. The cpDNA and mtDNA fragments were amplified using universal primers and subsequently digested with restriction enzymes to obtain the polymorphisms. Combinations of all the polymorphisms resulted in 33 cpDNA haplotypes and two mtDNA haplotypes. Strict association between the cpDNA haplotypes and the mtDNA haplotypes was detected in most cases, indicating conjoint inheritance of the two genomes. The most frequent and abundant cpDNA haplotype (C20; frequency, 51 %) is always associated with the more frequent and abundant mtDNA haplotype (M1; frequency, 84 %). All but two of the cpDNA haplotypes associated with the less frequent mtDNA haplotype (M2) are private haplotypes. These private haplotypes are phylogenetically related but geographically unrelated. They form a separate cluster on the minimum-length spanning tree.     

Structural analysis of chloroplast DNA in Prunus (Rosaceae): evolution, genetic diversity and unequal mutations

In order to understand the evolutionary aspects of the chloroplast DNA (cpDNA) structures in Rosaceous plants, a physical map of peach (Prunus persica cv. Hakuhou) cpDNA was constructed. Fourteen lambda phage clones which covered the entire sequence of the peach cpDNA were digested by restriction enzymes (SalI, XhoI, BamHI, SacI, and PstI) used singly or in combination. The molecular size of peach cpDNA was estimated to be about 152 kb. The gene order and contents were revealed to be equivalent to those of standard type of angiosperms by the localization of 31 genes on the physical map. Eighteen accessions from 14 Prunus species (P. persica, P. mira, P. davidiana, P. cerasis, P. cerasifera, P. domestica, P. insititia, P. spinosa, P. salicina, P. maritima, P. armeniaca, P. mume, P. tomentosa, P. zippeliana, and P. salicifolia) and one interspecific hybrid were used for the structural analysis of cpDNAs. Seventeen mutations (16 recognition site changes and one length mutation) were found in the cpDNA of these 18 accessions by RFLP analysis allowing a classification into 11 genome types. Although the base substitution rate in the recognition site (100p = 0.72) of cpDNA in Prunus was similar to that of other plants, i.e., Triticum–Aegilops, Brassica, and Pisum, it differed from Pyrus (100p = 0.15) in Rosaceae. Seven mutations including one length mutation were densely located within a region of about 9.1 kb which includes psbA and atpA in the left border of a large single-copy region of Prunus cpDNAs. The length mutation was detected only in P. persica and consisted of a 277 bp deletion which occurred in a spacer region between the trnS and trnG genes within the 9.1 kb region. Additional fragment length mutations (insertion/deletion), which were not detected by RFLP analysis, were revealed by PCR and sequence analyses in P. zippeliana and P. salicifolia. All of these length mutations occurred within the 9.1 kb region between psbA and atpA. This region could be an intra-molecular recombinational hotspot in Prunus species.     

Population genetic structure and conservation of the Azorean tree Prunus azorica (Rosaceae)

Prunus azorica is an endangered tree endemic to the Azores Archipelago, considered as a top priority species for conservation. Although propagation measures have been studied in detail, and a broad phylogeographic study on P. lusitanica was recently published, a detailed population genetics study devoted to Azorean taxon was lacking. To determine extant patterns of population genetic structure in P. azorica, we analysed eight populations from the five Azorean islands where the species presently occurs and the only extant individual from Flores Island. We also included samples of P. lusitanica subsp. hixa from the Canary Islands and Madeira, and of P. lusitanica subsp. lusitanica from mainland Portugal. Genotyping was undertaken for eight nuclear microsatellite polymorphic loci specifically isolated for P. azorica. Accessions of the different geographic regions were used to sequence ITS and trnL DNA regions. Regarding SSRs, the number of alleles ranged from 5 to 37 (mean = 12.6) per locus and from 2 to 64 per population (mean = 24). Our analysis showed a clear separation between samples from the Azores and those from other regions. Overall, São Miguel populations seemed to encompass the majority of the variability found within the archipelago. Regarding the Azorean populations only, the highest percentage of genetic variation was found within populations (92 %). Still, about 7 % of the variation was found among populations within islands. Expected heterozygosity ranged from values near 0 in the most depauperate populations up to 0.18. With a few exceptions, the level of differentiation between Azorean populations was generally low and gene flow was clearly above 1. Analysis of ITS sequences also detected differences between the Azores and the remaining regions but the trnL region did not reveal any variation. The genetic identity of P. azorica was recognised and thus should be preserved; however, the present results suggest that the Azorean taxon should be reinstated at the subspecies level.     

用叶绿体ndhF和核核糖体ITS序列推断李属(蔷薇科)的系统发育

Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to reconstruct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocera- sus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.     

A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA

The economically important plum or cherry genus (PRUNUS:) and the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Phylogenetic analysis using the ITS sequences of nuclear ribosomal DNA (nrDNA) was conducted to construct the evolutionary history and evaluate the historical classifications of PRUNUS: and the Amygdaloideae. The analyses suggest two major groups within the Amygdaloideae: (1) PRUNUS: s.l. (sensu lato) and MADDENIA:, and (2) EXOCHORDA:, Oemleria, and PRINSEPIA: The ITS phylogeny supports the recent treatment of including EXOCHORDA: (formerly in the Spiraeoideae) in the Amygdaloideae. MADDENIA: is found to be nested within PRUNUS: s.l. in the parsimony and distance analyses, but basal to PRUNUS: s.l. in the maximum likelihood analysis. Within PRUNUS:, two major groups are recognizable: (1) the AMYGDALUS:-PRUNUS: group, and (2) the CERASUS:-LAUROCERASUS:-PADUS: group. The clades in the ITS phylogeny are not congruent with most subgeneric groups in the widely used classification of PRUNUS: by Rehder. A broadly defined PRUNUS: is supported.     

Validation of Prunus hainanensis (Rosaceae)

The name Prunus hainanensis (G. A. Fu & Y. S. Lin) W. C. Chen is invalid because only the basionym was cited and without reference. According to the Art. 32.4 of ICBN, Prunus hainanensis (G. A. Fu et Y. S. Lin) H. Yu, N. H. Xia & H. G. Ye is the correct name. This new combination is proposed herein.     

Comparisons of within-population genetic variation in sexual and agamospermousAmelanchier (Rosaceae) using RAPD markers

We compared genetic variation of sexualAmelanchier bartramiana and facultatively agamospermous (asexually seed-producing)A. laevis at one site where the two species are sympatric. We analyzed 77 random amplified polymorphic DNA (RAPD) markers in 29A. bartramiana individuals and 76 RAPD markers in 31A. laevis individuals. The two species do not differ significantly in mean genetic variation. However, 22.4% of genetic similarity values betweenA. laevis individuals exceed the highest value ofA. bartramiana and may represent the effect of agamospermy. Variation withinA. laevis may be the result of sexuality, hybridization, polyploidy, and other factors.     

Population genetic analysis and origin discrimination of snow crab (Chionoecetes opilio) using microsatellite markers

Major habitats for the snow crab Chionoecetes opilio are mostly found within the northwest Atlantic and North Pacific Oceans. However, the East Sea populations of C. opilio, along with its relative the red snow crab (C. japonicas), are two of the most important commercial crustacean species for fisheries on the east coast of the Korean Peninsula. The East Sea populations of C. opilio are facing declining resources due to overfishing and global climate change. Thus, an analysis of population structure is necessary for future management. Five Korean and one Russian group of C. opilio were analyzed using nine microsatellite markers that were recently developed using next-generation sequencing. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The number of alleles per locus varied from 4 to 18 with a mean of 12, and allelic richness per locus ranged from 4.0 to 17.1 across all populations with a mean of 9.7. The Hardy–Weinberg equilibrium test revealed significant deviation in three out of nine loci in some populations after sequential Bonferroni correction and all of them had higher expected heterozygosity than observed heterozygosity. Null alleles were presumed in four loci, which explained the homozygosity in three loci. The pairwise fixation index (F _ST ) values among the five Korean snow crab populations did not differ significantly, but all of the pairwise F _ST values between each of the Korean snow crab populations and the Russian snow crab population differed significantly. An UPGMA dendrogram revealed clear separation of the Russian snow crab population from the Korean snow crab populations. Assignment tests based on the allele distribution discriminated between Korean and Russian origins with 93 % accuracy. Therefore, the snow crab populations around the Korean Peninsula need to be managed separately from the populations in Bering Sea in global scale resource management. Also, this information can be used for identification of snow crab origin which is problematic in worldwide crab trade.     

Molecular phylogeny and genetic diversity of Tunisian Quercus species using chloroplast DNA CAPS markers

Chloroplast DNA variation was studied in five evergreen Quercus species from the Western part of Tunisia using Cleaved Amplified Polymorphic Sequence (CAPS) technique. Five primer pair/endonuclease combinations have been used. Chlorotypes of Quercus species have been identified. The enzyme HinfI was more efficient in detecting polymorphism in oak species than TaqI. The phenogram showed five groups defining the five studied oak species: suber group, afares group, coccifera group, canariensis group and ilex group. The topology of phenogram showed that the classification depends only on species and independently of their geographic origin. The principal component analysis (ACP) corroborated the results of the tree branching and confirmed the existence of five species groups. Our results showed a genetic proximity between Quercus afares and Quercus coccifera species that may be due to temperature tolerance or the demographic history of these species. Nevertheless, a high value of G_ST calculated (G_ST = 1), suggesting that the maximum of variation is maintained among oak species. This result was confirmed by the low value of the genetic diversity within species (h_S = 0), the value obtained of the total genetic diversity (h_T = 0.378) and the absence of gene flow between species (N_m = 0). A high genetic proximity has been registered between Q. afares, Quercus suber and Quercus canariensis. Moreover, Q. afares shared the chlorotype of Q. suber and Q. canariensis which suggests its hybrid origin.     

Chloroplast DNA phylogeny and phylogeography of the North American plums (Prunus subgenus Prunus section Prunocerasus, Rosaceae)

The North American plums are a closely related group that are not easily circumscribed, have overlapping morphologies, and are known to hybridize. We previously showed that the North American plums are a closely related, monophyletic group of taxa with little to no cpDNA sequence divergence between taxa. In that study, we came to the unanticipated conclusion that relationships inferred among the taxa contrast sharply with previously defined groups based on morphological characters. Here the aim was to determine if the primary cpDNA haplotypes identified in our earlier study are confined to the taxa in which they were initially observed. The cpDNA rpL16 intron was sequenced for 207 accessions of the 17 North American plum taxa plus Prunus texana. The results show that many taxa contain more than one of the three primary cpDNA haplotypes. Aside from the results found in sect. Prunocerasus, this study has broader implications for phylogenetics in general. The common practice of choosing a single exemplar to represent a taxon can be profoundly misleading in closely related groups. In hindsight, the possibility existed in our earlier study that we could have chosen a different combination of exemplars, which could have resulted in a different inferred phylogeny.     

Selective fruit abortion in Prunus mahaleb (Rosaceae)

In Prunus mahaleb (Rosaceae), only a small proportion of those flowers that initially develop give rise to fruits, and the probability of producing fruit differs between flowers. The results of this study indicate that the probability of producing fruit is about 60% for the first (i.e., most proximal) flower to develop in each inflorescence, but very low for the last (i.e., most distal). This pattern is maintained regardless of between-inflorescence differences in flowering phenology, suggesting that each inflorescence can be viewed as an independent subunit with respect to allocation of resources for reproduction. These results are compatible with the ovary reserve and selective abortion hypotheses for the adaptive value of low fruit set in P. mahaleb.     

Population genetic analysis of white shrimp,Litopenaeus setiferus,using microsatellite genetic markers

The white shrimp (Litopenaeus setiferus) is a commercially and recreationally valuable species, yet little is known of its population structure or genetic diversity. White shrimp are distributed along the Atlantic coast of the United States and from the west coast of Florida to the Bay of Campeche, Mexico. In this study, shrimp were collected from North Carolina, South Carolina (four separate collections were taken from 1995 to 1999), Georgia, the Atlantic and Gulf coasts of Florida, Louisiana, Texas and Mexico. DNA was isolated from these individuals, and genetic variation was assessed at six microsatellite loci. These loci were, for the most part, highly polymorphic with an average expected heterozygosity of 0.68. Deviations from Hardy-Weinberg proportions were observed over all samples, but experimental results suggested the presence of null alleles, which confounded a biological interpretation of this result. Pairwise tests of the similarity of allele frequency distributions and distance measure analyses showed broad-scale genetic homogeneity superimposed over occasional indications of random geographical and temporal differentiation. FST and RST estimates over all loci and samples were 0.002 or less and indicated little population structure. Weak but significant genetic differentiation was evident only between pooled western Atlantic and pooled Gulf of Mexico samples. Within the Gulf of Mexico or within the western Atlantic, the large-scale genetic homogeneity observed may be a consequence of genetic mixing resulting from pelagic larvae and adult migrations, while the random local genetic differentiation may be a result of genetic sampling or experimental sampling error. The weak differentiation between shrimp from the Gulf of Mexico and the western Atlantic can be explained by a relatively recent separation of these two populations and/or small amounts of ongoing gene flow.     

Phylogeny and Classification of Prunus sensu lato （Rosaceae）

The classification of the economically important genus Prunus L. sensu lato （s.L） is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.I. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions （atpB- rbcL, matK, ndhF, psbA-trnH, rbcL, rpL 16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycfl） and three nuclear genes （ITS, s6pdh and Sbel） to explore their infrageneric used to develop a new, phylogeny-based classification relationships. The results of these analyses were of Prunus s.I. Our phylogenetic reconstructions resolved three main clades of Prunus s.I. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades： subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae （T. T. yu ＆ L. T. Lu） S. L. Zhou and one new species name, Prunus tianshanica （Pojarkov） S. Shi, were proposed.     

Merging Maddenia with the morphologically diverse Prunus (Rosaceae)

Maddenia (Rosaceae) has been distinguished from Prunus on the basis of its tepaloid perianth and one‐ to two‐carpellate gynoecium. These distinctive morphological traits nonetheless overlap with several Prunus spp. Maddenia has previously been shown to be nested within Prunus, more specifically within a clade containing members of subgenera Laurocerasus and Padus, but its phylogenetic position within that clade has not been defined precisely. This study clarifies the position of Maddenia within Prunus through phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and plastid ndhF sequences, with an expanded sampling of tropical species of subgenus Laurocerasus and the inclusion of three Maddenia spp. The monophyly of Maddenia is supported by both the ITS and ndhF analyses, but both datasets support the inclusion of Maddenia in Prunus. All trees from the ITS analysis and some trees from the ndhF analysis also support a close alliance of Maddenia with a clade comprising temperate species of subgenera Laurocerasus and Padus. On the basis of these results, all recognized species of Maddenia are herein formally transferred to Prunus, which requires four new combinations and one new name: Prunus fujianensis (Y.T.Chang) J.Wen, comb. nov. ; Prunus himalayana J.Wen, nom. nov. ; Prunus hypoleuca (Koehne) J.Wen, comb. nov. ; Prunus hypoxantha (Koehne) J.Wen, comb. nov. ; and Prunus incisoserrata (T.T.Yü & T.C.Ku) J.Wen, comb. nov. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 236–245.     

Random amplified polymorphic DNA (RAPD) markers for genetic analysis inAllium

RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative of onion (A. roylei), were evaluated for variability using a set of 20 random 10-mer primers. Seven out of the twenty primers revealed scorable polymorphisms between cultivars ofA. cepa and these will be further evaluated for use in genetic mapping. Wide variations in banding profiles between species were observed with nearly every primer tested. These were assessed for use in systematic studies within the genus. Ninety-one band positions were scored (+/-) for all the cultivars studied. Genetic distances between each of the cultivars were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them. The resulting analysis was in broad agreement with previous classifications of the species studied, confirming the validity of the method. However, amongst the species studied, it placedA. roylei as the closest relative ofA. cepa, questioning the current classification of the former species in the section Rhizideum.     

Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP

BACKGROUND AND AIMS: The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. METHODS: Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. KEY RESULTS: In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. CONCLUSIONS: The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence.     

Addressing the "hardest puzzle in American pomology:" Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions

Prunus subg. Prunus sect. Prunocerasus (Rosaceae) is a North American taxon with 17 commonly recognized taxa. To test the hypothesis of monophyly for the section we sequenced the trnG and rpL16 introns and the trnH-psbA and trnS-trnG intergenic spacers for at least two representatives of each of the five subgenera in Prunus. Additionally we sampled heavily among Prunus subg. Prunus sections Prunus and Armeniaca and Prunus subg. Amygdalus because these groups are putatively most closely related to Prunocerasus. Once monophyly of sect. Prunocerasus was shown we added the sequences of trnL and rpS16 introns and the trnL-trnF spacer in an attempt to increase resolution within the section. The species of sect. Prunocerasus showed an initial split with P. subcordata, the only species from western North America, sister to the rest of the group. The remaining species fell into three primary clades. Within each of the three primary clades there was little phylogenetic resolution. Lastly, we present evidence that P. texana, previously classified in subg. Amygdalus, may be a plum or at least contain a Prunocerasus chloroplast. This is the first phylogenetic hypothesis presented for sect. Prunocerasus, and the clades recovered contrast sharply with previously defined groups based on morphological characters.     

Population genetic analysis among five Indian population groups using six microsatellite markers

Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.     

Population structure and genetic diversity of Lithocarpus litseifolius (Fagaceae) assessed using microsatellite markers

Lithocarpus litseifolius (Fagaceae), known as tree of Chinese sweet tea, is a native commercial plant distributed in south China and adjacent areas. This study used ten microsatellite markers to investigate the genetic variation and population structure of 11 populations of L. litseifolius from the main production regions in China. All of the tested loci proved to be effective for the species. The number of alleles per locus ranged between 3 and 39, and mean observed and expected heterozygosity was 0.43 and 0.52, respectively. The deficiency in heterozygosity may be the result of human interference and harvesting activities. Analysis of molecular variance revealed that most of the variation was within populations, whereas differentiation among populations was insignificant, and that there was no significant correlation between genetic distance and geographic distance (r = 0.4089, p = 0.9940). However, A Bayesian model‐based analysis sorted all 11 populations into two (when k = 2) or three (when k = 3) clusters with higher probabilities and showed a geographical pattern which is probably related to the topography of China. Our results provide important information for protecting, sustainably using, and improving the current resources of L. litseifolius.