Chloroplast Rpl16 Intron Research Articles

Assessing the maternal origin in the polyploid complex of Camellia reticulata based on the chloroplast rpl16 intron sequences: implications for camellia cross breeding

Camellia reticulata is a well-known woody ornamental species endemic to Southwest China. It represents a polyploid complex with diploids, allotetraploids, and allohexaploids. The parentage of the allotetraploids and allohexaploids has been reported by genomic in situ hybridization, but the maternal parents still remain unknown. In this study, sequences of the chloroplast rpl16 intron of 105 cultivars of C. reticulata and 7 congeneric species were used to infer the maternal origin of the allopolyploids. The results showed that (1) the allotetraploids were derived from C. pitardii as the maternal parental species and the diploid C. reticulata as the paternal parental species; (2) the allohexaploid C. reticulata was derived from the allotetraploid C. reticulata as the maternal parent and C. saluenensis as the paternal parent; and (3) the C. reticulata cultivars were derived from hexaploid C. reticulata as the maternal parents. These results indicated that C. pitardii, the allotetraploid and allohexaploid C. reticulata may serve as good potential maternal parents for the cross breeding of Camellia.

An assessment of tissue culture-induced genetic variability in olive (Olea europaea L.) using chloroplast rpl16 intron sequences and single primer amplification reaction (SPAR) markers

SUMMARYOlive (Olea europaea L.) is an important tree crop grown throughout the Mediterranean Basin and Iran. Propagation of true-to-type olive plants is important for olive-growing companies and farmers. For this reason, we performed a genetic analysis of 49 randomly selected tissue culture-regenerated olive plants of the cultivar ‘Koroneiki’ and compared them with the mother plant. We used the sequence of the chloroplast rpl16 intron and ten single primer amplification reaction (SPAR) markers to test for genetic fidelity vs. somaclonal variation. A Neighbor-Joining dendrogram based on the RAPD data produced four major clusters. The mother plant, along with ten regenerated plants, were placed far from the others and formed Cluster I. Members of this Cluster had the highest genetic distance from members of Cluster III (0.266), followed by plants of Cluster IV (0.177). Analysis of molecular variance (AMOVA) produced significant differences (PhiPT value = 0.37; P≤ 0.01) among these clusters. The Neighbor-Joining tree, neighbor-Net method, and Tree analysis using New Technology (TNT) based on RAPD marker and rpl16 intron sequence analyses respectively, separated the mother plant and some of the regenerated plants in a separate cluster. Tajima's test produced a diversity (D) statistic value of = −2.17 (P ≤ 0.05) based on the intron sequence data. We also identified some regenerated plants that were true-to-type with the mother plant.

Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora.

BackgroundThe picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.ResultsExcept for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.ConclusionsBased on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-55-1) contains supplementary material, which is available to authorized users.

C3 photosynthesis in Aristida longifolia: Implication for photosynthetic diversification in Aristidoideae (Poaceae)

Only a small percentage of plant species undergo C(4) photosynthesis. Despite its rarity, the C(4) pathway has evolved numerous times from C(3) ancestors, with as many as 18 independent origins in grasses alone. We report non-Kranz (C(3)) anatomy in Aristida longifolia, a species in a genus of ca. 300 species previously thought to possess only Kranz (C(4)) anatomy. Leaf blade transections of A. longifolia show widely spaced vascular bundles, nonradiate chlorenchyma, and few or no chloroplasts in cells of the sheaths surrounding the vascular bundle, all features indicative of C(3) photosynthesis. Carbon isotope ratios range from -27.68 to -29.71%, likewise indicative of C(3) photosynthesis. We also reconstruct the phylogeny of Aristidoideae, comprising Aristida, Sartidia (C(3)), and Stipagrostis (C(4)), using a sample of 11 species, including A. longifolia, and DNA sequences of the nuclear ribosomal internal transcribed spacer region and the chloroplast rpl16 intron and trnL-trnF region. Sartidia and Stipagrostis resolve as sisters, and sister to this clade is Aristida. Aristida longifolia resolves as sister to the remaining species in the genus. C(3) photosynthesis is hypothesized to be ancestral in Aristidoideae, which means the C(4) pathway evolved twice in the subfamily-in Stipagrostis and early in the diversification of the Aristida clade.

Successful DNA amplification of a more than 200‐year‐old herbarium specimen: recovering genetic material from the Linnaean era

AbstractThe limit for successful DNA extraction was tested by amplification and sequencing of an over 200‐year‐old herbarium specimen collected by Adam Afzelius, a student of Carl Linnaeus. We amplified and sequenced a 800‐bp region between 16S ribosomal DNA and the 3′ part of the trnI gene (16S‐trnI) in the chloroplast genome of Phaulopsis talbotii S. Moore (Acanthaceae). To test the replicability and to control for contamination the procedure was performed in sealed vials and with negative PCR controls. The procedure was also repeated in a separate laboratory. In addition, the chloroplast rpl16 intron was successfully amplified and sequenced and the rps16 intron amplified. Sequences of taxa closely related to Acanthaceae were found to be most similar to the produced sequences. The results suggest that molecular investigations of other 18th century botanical collections are feasible and that molecular methods could be employed for comparative studies to extant plant collections. An important application would be to identify descendants or clones of Linnaean lectotypes by comparing DNA from these with potentially remnant plants from Linnaeus' cultivations.

Phylogeny and Character Evolution in Nierembergia (Solanaceae): Molecular, Morphological, and Cytogenetic Evidence

Nierembergia (Solanaceae) contains 21 species found primarily in South America, with one species occurring disjunctly in Mexico. Among other features, a pollination system not found elsewhere in the Solanaceae typifies this genus. In most species, nectaries are absent, but oil-producing elaiophores are present on the corolla limb and these attract oil-collecting bees. Molecular phylogenetic hypotheses based on nuclear ITS and chloroplast rpl16 intron data support the monophyly of Nierembergia, which is sister to a clade composed of Bouchetia plus Hunzikeria. The data reconstruct two clades within the genus: one composed primarily of herbaceous species with broad stigmas and the second containing woody species with crescent-shaped stigmas. Morphological homoplasy is frequent among the species of the herbaceous clade, while the woody clade is morphologically cohesive. Chromosome counts are confirmed and karyotype features are given for 13 Nierembergia species (including six varieties) and for Bouchetia anomala, Leptoglossis linifolia, and Petunia axillaris. The two clades are also supported by karyotypic features: one has asymmetrical karyotypes, small chromosomes, and two chromosome pairs with nucleolar organizing regions (NOR) and the other has symmetrical karyotypes, large chromosomes, and only one NOR.

THE DIVERSIFICATION OF HALENIA (GENTIANACEAE): ECOLOGICAL OPPORTUNITY VERSUS KEY INNOVATION

The plant genus Halenia (Gentianaceae) consists of herbs growing in temperate and tropical alpine habitats and most species possess flowers in which nectar is produced in spurs. This probably helps reward only specialized long-tongued pollinators, and a narrow pollinator/flower relationship is thought to accelerate diversification rates (a key innovation). To test the pattern of diversification of Halenia against the unspurred sister group we reconstructed phylogenetic relationships among 22 species plus outgroups using nuclear ITS and chloroplast rpl16 intron sequence data. We show that Halenia originated in East Asia and migrated via North America into Central America. From there, it colonized South America three times independently, probably within the last million years. Significant changes in diversification rates were found during the evolution of Halenia using a sister group method, a likelihood method, and a diversity-through-time plot. In contrast to other studies, we could not observe a direct speciation rate effect of the evolution of nectar spurs in comparison with the unspurred sister group of Halenia. Rather, increases in diversification occurred following the colonization of Central and South America by spurred progenitor taxa. This later switch in diversification may have resulted from the availability of new geographical and ecological opportunities, or from the availability of more and different pollinators in these regions. Following the latter hypothesis, the nectar spurs were a preadaption and functioned as a key innovation only in this new biotic environment. After an initial rapid increase, a reduction in diversification rate was observed in Central America, probably illustrating density dependence of speciation rates. Finally, we found preliminary evidence for the key innovation hypothesis in geologically young spurred and unspurred lineages of Halenia in South America.

THE DIVERSIFICATION OF HALENIA (GENTIANACEAE): ECOLOGICAL OPPORTUNITY VERSUS KEY INNOVATION

The plant genus Halenia (Gentianaceae) consists of herbs growing in temperate and tropical alpine habitats and most species possess flowers in which nectar is produced in spurs. This probably helps reward only specialized long-tongued pollinators, and a narrow pollinator/flower relationship is thought to accelerate diversification rates (a key innovation). To test the pattern of diversification of Halenia against the unspurred sister group we reconstructed phylogenetic relationships among 22 species plus outgroups using nuclear ITS and chloroplast rpl16 intron sequence data. We show that Halenia originated in East Asia and migrated via North America into Central America. From there, it colonized South America three times independently, probably within the last million years. Significant changes in diversification rates were found during the evolution of Halenia using a sister group method, a likelihood method, and a diversity-through-time plot. In contrast to other studies, we could not observe a direct speciation rate effect of the evolution of nectar spurs in comparison with the unspurred sister group of Halenia. Rather, increases in diversification occurred following the colonization of Central and South America by spurred progenitor taxa. This later switch in diversification may have resulted from the availability of new geographical and ecological opportunities, or from the availability of more and different pollinators in these regions. Following the latter hypothesis, the nectar spurs were a preadaption and functioned as a key innovation only in this new biotic environment. After an initial rapid increase, a reduction in diversification rate was observed in Central America, probably illustrating density dependence of speciation rates. Finally, we found preliminary evidence for the key innovation hypothesis in geologically young spurred and unspurred lineages of Halenia in South America.

Phylogeny of the Madagascan endemic family Didiereaceae

A molecular phylogeny of the Didiereaceae was produced through parsimony analysis of chloroplastrpl16 intron andtrnL-trnF andtrnT-trnL intergenic spacer sequences of all eleven species of the Didiereaceae and several outgroup taxa from the Portulacaceae. Results indicated that: 1) the Didiereaceae were embedded within the Portulacaceae, withCalyptrotheca as the sister group of the family; 2) present generic limits were supported; 3)Alluaudiopsis was the most basal lineage; 4) at least two separate episodes of polyploidization within the genusAlluaudia had occurred, and 5) unusually low amounts of variation were present in rapidly evolving noncoding plastid sequences.

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets.

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.

Low Levels of Intraspecific Genetic Variation at a Rapidly Evolving Chloroplast DNA Locus in North American Duckweeds (Lemnaceae)

Although most previous studies on chloroplast (cp) DNA variation in plants have concentrated on systematics and evolution above the species level, intraspecific variation in cpDNA is common and has provided useful insights into population-level evolutionary processes. Polymerase chain reaction methods were used to examine restriction site and sequence variation in the chloroplast rpLI6 gene within and among populations of duckweed species (Spirodela and Lemna) from the southern and eastern United States. To our knowledge, the rpL16 region has not previously been used to investigate cpDNA variation in nature. While considerable restriction site and sequence variation were detected among species, no variation was found within populations of either of the two species (S. punctata and L. minor) selected for sequence analysis, and S. punctata showed no interpopulational variation. Two cpDNA haplotypes were identified in L. minor, with one haplotype restricted to three sites in Louisiana and the other found in all other populations sampled. This paucity of variation cannot be readily explained as the result of a low mutation rate. In general, group II introns appear to be subject to very little functional constraint, and extensive sequence differences have been found between species in the chloroplast rpL16 intron in particular. However, factors such as historical range expansions and contractions, founding effects, fluctuations in local population size, and natural selection may play a role in reducing cpDNA sequence variability in these species.

Low levels of intraspecific genetic variation at a rapidly evolving chloroplast dna locus in North American duckweeds (Lemnaceae)

Although most previous studies on chloroplast (cp) DNA variation in plants have concentrated on systematics and evolution above the species level, intraspecific variation in cpDNA is common and has provided useful insights into population‐level evolutionary processes. Polymerase chain reaction methods were used to examine restriction site and sequence variation in the chloroplast rpLI6 gene within and among populations of duckweed species (Spirodela and Lemna) from the southern and eastern United States. To our knowledge, the rpL16 region has not previously been used to investigate cpDNA variation in nature. While considerable restriction site and sequence variation were detected among species, no variation was found within populations of either of the two species (S. punctata and L. minor) selected for sequence analysis, and S. punctata showed no interpopulational variation. Two cpDNA haplotypes were identified in L. minor, with one haplotype restricted to three sites in Louisiana and the other found in all other populations sampled. This paucity of variation cannot be readily explained as the result of a low mutation rate. In general, group II introns appear to be subject to very little functional constraint, and extensive sequence differences have been found between species in the chloroplast rpL16 intron in particular. However, factors such as historical range expansions and contractions, founding effects, fluctuations in local population size, and natural selection may play a role in reducing cpDNA sequence variability in these species.