Analyses Of Chloroplast DNA Sequences Research Articles

Investigation of the variability of chloroplast DNA of some Astragalus spp. of sect. Helmia and A. arcanus of sect. Erioceras (Fabaceae)

Analysis of chloroplast DNA sequences revealed a high polymorphism of the length and nucleotide composition of trnF–trnV and the intron trnL for Helmia section species of the genus Astragalus (Fabaceae). Molecular genetic studies of Astragalus species of the Helmia section were previously practically not carried out; sequencing of trnF–trnV and the intron trnL of chloroplast DNA for 7 species of the section, as well as the probable intersection hybrid Astragalus arcanus held for the first time. On the basis of genetic studies, clarified the relationship between species included in the section Helmia. The possible stages of sect. Helmia evolution are discussed. The taxonomic isolation of Astragalus permiensis has been confirmed; it is assumed not to be of Uralic, but of Siberian or Central Asian origin. Astragalus ionae belongs to the section Helmia is confirmed. Astragalus depauperatus s. l. is thought to be a complex of twin species. In this article, one of them is considered in the status of the species A. chakassiensis. 
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Tmesipteris alticola (Psilotaceae), a new fern species endemic to New Caledonia

ABSTRACT Tmesipteris alticola is described here as a new fern species endemic to New Caledonia's Grande Terre. It is a fifth species of Tmesipteris for the territory, and the second endemic. The obovate leaves and conic synangia of T. alticola distinguish it morphologically from all other species of Tmesipteris. Phylogenetic analyses of chloroplast DNA sequences support its distinctiveness, and indicate it is most closely related to T. truncata and T. vieillardii among the sampled species. Tmesipteris alticola is known from only four mountainous locations, all with ultramafic substrates in Province Sud, at elevations of 1200 m–1500 m, where it grows terrestrially or as a low epiphyte, seemingly mostly on ridges or around summits within short-statured cloud forest. We propose a provisional IUCN conservation status of Near Threatened for T. alticola because of its limited known occurrences. Tmesipteris alticola adds to a slew of fern species that have been recently newly described, reinstated, or recorded in New Caledonia.

New records of fern species from New Caledonia in the genera Davallia, Dicranopteris, Dryopteris, Pteris, and Trichomanes

ABSTRACT Six fern species are newly reported or substantiated as indigenous to New Caledonia: Davallia sessilifolia, Dicranopteris caudata, Dryopteris arborescens, Pteris terminalis, Trichomanes atrovirens, and T. kurzii. This is the first record of Dryopteris for New Caledonia. Our findings are based on extensive fieldwork, inspection of specimens in relevant herbaria including type material, comparisons with authoritative references, and phylogenetic analyses of chloroplast DNA sequences. The global and New Caledonian distribution, morphological diagnosis, and conservation status are given for each species. Davallia sessilifolia, Dryopteris arborescens, Pteris terminalis, and Trichomanes atrovirens are provisionally assessed as Critically Endangered or Endangered in New Caledonia, because they have few populations that are each of limited size, and some are also threatened by fire or introduced deer and pigs. While Dicranopteris caudata occurs in open habitats, the others are largely confined to humid habitats at high elevation, or to the wetter forested valleys of north-east Grande Terre. These are the most likely habitats in which to find more populations of these species, but also other new species records and new endemic ferns. Alongside the recent description of several new endemic species, the addition of so many non-endemic indigenous species to a fern and lycophyte flora of approximately 300 species is an indication that considerable work remains to be done in documenting these plants in New Caledonia.

Reinstatement of the New Caledonian endemic fern Blechnum deplanchei as distinct from B. opacum (Blechnaceae)

ABSTRACT Blechnum opacum is a small forest fern indigenous to New Caledonia and Vanuatu. After examining the considerable morphological variation in New Caledonian populations, along with phylogenetic analysis of chloroplast DNA sequences, we conclude that B. deplanchei should be reinstated for some of the plants in New Caledonia. Blechnum deplanchei is readily recognisable, with pinnatisect fronds that are usually larger, pinnae that are numerous and oblong, and with the distal lamina segments reduced in size. Based on two chloroplast loci, the three sampled populations of B. deplanchei comprised a distinct and well-supported lineage. The genetic and morphological distinctiveness of B. deplanchei was maintained over a reasonably large area, including areas of broad sympatry with B. opacum. Blechnum deplanchei is largely confined to the mountains in southern Grande Terre, in areas underlain by ultramafic substrates. It generally occurs at higher elevations, and is assessed with a conservation status of Near Threatened. Even with the recognition of B. deplanchei, B. opacum remains a variable species. A few plants are morphologically intermediate. We provisionally retain them in B. opacum, but they require further investigation. The morphologically intermediate samples in the phylogenetic analyses were the most distantly related among the ingroup, contributing to the paraphyly of B. opacum with respect to B. deplanchei. The morphologically intermediate plants are unlikely to be first generation hybrids or allopolyploids, given their genetic distinctiveness, the regularity and comparable size of their spores, and because some occur far to the north of the distribution of B. deplanchei; furthermore, Vanuatu plants have a similar morphology. It is possible that they may simply be unusually large plants of B. opacum, or a distinct, third species. Resolving their status requires genetic analysis of additional samples from northern Grande Terre and Vanuatu. With the circumscription adopted here, we assess B. opacum as Least Concern.

Lastreopsis abscondita (Dryopteridaceae), a new fern species endemic to New Caledonia

ABSTRACT The fern genus Lastreopsis has been recently re-circumscribed to include about 19 species. It occurs from southern Asia through the Pacific to the Neotropics, with Australasia having the most species. We here describe a new species endemic to New Caledonia’s Grande Terre, L. abscondita. Morphological comparisons and phylogenetic analyses of chloroplast DNA sequences show that L. abscondita resembles and is closely related to L. vieillardii, also endemic to New Caledonia. From L. vieillardii, L. abscondita differs most noticeably in being much scalier, particularly on its rachis and costae, and in having larger scales, and larger, more-divided fronds. Chloroplast DNA sequences distinguish samples of L. abscondita as a clade, but indicate there is substantial genetic variation within the narrowed circumscription of L. vieillardii such that it is paraphyletic; this should be further investigated. Lastreopsis abscondita is known from only two sites, both at high elevation on non-ultramafic substrates on Grande Terre. We propose an IUCN conservation status of Vulnerable for L. abscondita, particularly because of the small number of sites and limited area of occupancy. The specific epithet alludes to the fact that this large fern, with fronds over 1.5 m long, has been overlooked until now. This is another indication that the ferns of New Caledonia warrant further study, with more discoveries likely to be made.

The phylogenetic position of Aglaodorum Schott (Araceae – Aroideae – Aglaonemateae)

Analysis of chloroplast DNA sequences (trnL intron and trnLtrnF intergenic spacer) of the helophytic colony-forming Aglaodorum griffithii (Schott) Schott and other representative species of Araceae supported its placement within Aglaonema Schott. It is therefore proposed that Aglaodorum Schott should be recognised as a generic synonym of Aglaonema.

Hiya distans (Dennstaedtiaceae), a new combination for an Australasian fern previously classified in Hypolepis

ABSTRACTThree tropical fern species previously treated in the Dennstaedtiaceae genus Hypolepis were recently segregated in a new genus, Hiya, based on phylogenetic analysis of chloroplast DNA sequences and assessment of their morphology. That study specifically mentioned the uncertain placement of the Australasian species Hypolepis distans, which has long been regarded as anomalous within Hypolepis. Using phylogenetic analysis of rbcL and rpl16 sequences, along with morphological and cytological characters, we show that Hypolepis distans is best placed in Hiya, and make the new combination Hiya distans. However, this requires a significant adjustment in the morphological characterisation of Hiya. It can be recognised by the adaxial sulcus of the primary pinnae being confluent with the rachis, veins which reach the lamina margin at an indentation, and the primary pinnae arising at ± 90° from the rachis. It is also a significant ecological extension of Hiya, from the tropical highlands of Malesia and Central and South American to the lowlands of temperate Australasia.

Origin and Dispersal of Domesticated Peach Palm

Peach palm (Bactris gasipaes Kunth) is the a Neotropical palm domesticated by Native Americans. Its domestication resulted in a set of landraces (var. gasipaes), some with very starchy fruit used for fermentation, others with an equilibrium of starch and oil used as snacks. Which of the three wild types (var. chichagui) was involved and where the domestication process began are unclear, with three hypotheses under discussion: an origin in southwestern Amazonia; or in northwestern South America; or multiple origins. We reevaluate one of the wild types, defining it as the incipient domesticate, and then evaluate these hypotheses using the Brazilian peach palm Core Collection and selected herbaria samples to: 1) model the potential distributions of wild and domesticated populations; 2) identify the probable origin of domestication with a phylogeographic analysis of chloroplast DNA sequences; and 3) determine the dispersal routes after domestication using spatial analysis of genetic diversity based on 17 nuclear microsatellite loci. The two very small-fruited wild types have distinct distributions in the northern Andes region and across southern Amazonia, both under moderately humid climates, while the incipient domesticate, partly sympatric with the southern wild type, is also found along the Equatorial Andes, in a more humid climatic envelope, more similar to that of the domesticated landraces. Two distribution models for Last Glacial Maximum conditions (CCSM4, MIROC) also suggest distinct distributions for the two wild populations. The chloroplast DNA phylogeographic network confirms the area of sympatry of the incipient domesticate and the southern wild type in southwestern Amazonia as the origin of domestication. The spatial patterns of genetic diversity confirm the proposal of two dispersals, one along the Ucayali River, into western Amazonia, northwestern South America and finally Central America; the other along the Madeira River into central and then eastern Amazonia. The first dispersal resulted in very starchy fruit for fermentation, while the second may have been later and resulted in snack fruits. Further explorations of southwestern Amazonia are essential for more precise identification of the earliest events, both with new archaeological methods and genetic analyses with larger samples.

Comparative analysis of chloroplast DNA sequences of Codonopsis lanceolata and Platycodon grandiflorus and application in development of molecular markers

Codonopsis lanceolata and Platycodon grandiflorus (order Asterales) originate from East Asia. Despite the high commercial availability of C. lanceolata and P. grandiflorus, limited genetic research has been performed on these plants. We applied a targeting enrichment method to detect genetic diversity in C. lanceolata and P. grandiflorus and recovered their chloroplast genomes from total DNA sequence data. Chloroplast DNAs (cpDNAs) were 61,154 bp (C. lanceolata) and 81,214 bp (P. grandiflorus) in length. Sixteen simple sequence repeats and 15 long repeat sequences were determined, which are useful as potential markers in both plant species. We surveyed the phylogenetic relationships with increased resolution in 14 plant species, including other 8 species from the order Asterales and 4 from the order Apiales. In addition, we demonstrated the availability of recovered chloroplast genomes through cpDNA marker development to determine the authenticity of food fraud at the DNA level of plant species.

Naturally occurring triploid hybrids between Miscanthus sacchariflorus and M. sinensis in Southern Japan, show phenotypic variation in agronomic and morphological traits

Miscanthus × giganteus, a triploid hybrid between tetraploid M. sacchariflorus and diploid M. sinensis, is considered to be a promising biomass crop for producing renewable bioenergy in temperate regions. However, because most cultivars of the hybrid have been derived from a single clone through vegetative propagation, genetic resources with diverse phenotypes are required to allow adaptation to changing environments and resistance to pests and diseases. The present study aimed to identify novel natural hybrids between M. sacchariflorus and M. sinensis and to assess their natural variation in agronomic and morphological traits. We have identified 51 Miscanthus plants with nuclear DNA content of triploid Miscanthus within a 5-km radius of the Kikuchigawa River basin located in southern Japan. Seven spontaneous triploids, including five representative strains in the Kikuchigawa River basin, had the chromosome number and nuclear DNA content comparable with those of triploid M. × giganteus, and showed the amplification of species-specific DNA fragments from both parent species in DNA marker analysis. These demonstrated that these spontaneous strains were natural triploid hybrids. A 2-year-long field experiment in a warm climate revealed that these triploid hybrids showed phenotypic variation in agronomic and morphological traits. In addition, phylogenetic analysis of chloroplast DNA sequences revealed that these triploid hybrids had a polyphyletic origin but that all seven hybrids contained cytoplasm from M. sacchariflorus. The present study suggests that naturally occurring triploid hybrids could be more widely distributed in southern Japan than previously reported and be important breeding resources to develop Miscanthus cultivars with novel characteristic traits.

Microsatellite and chloroplast DNA analyses reveal no genetic variation in a beach plant Surianana maritima on the Paracel Islands, China

Genetic variation within and among six natural populations of beach plant Suriana maritima on the Paracel Islands of China was assessed using SSR and chloroplast DNA sequence analysis. The results showed a complete absence of genetic variation between individuals either within or among populations. The cumulative consequences of a founder effect, selfing, and inbreeding may be responsible for the loss of genetic diversity in S. maritima.

Distribution and Phylogeography of <i>Caryopteris incana</i> (Lamiaceae) Based on Chloroplast DNA Sequences in West Kyushu, Japan

Caryopteris incana is a continental plant, transferred to Japan from continental Asia via a land bridge between the Korean Peninsula and Tsushima Islands during a glacial period. It currently grows wild in West Kyushu, Japan. In a previous study, we investigated the distribution of C. incana in the Tsushima Islands and confirmed the genetic structure of populations by using chloroplast DNA sequence analysis, suggesting that different haplotypes were distributed in the same area. Thus, it seemed that populations of C. incana throughout the Tsushima Islands colonized at different times; each haplotype had remained within its population without mixing. In this study, we conducted fieldwork to construct a detailed distribution map in West Kyushu excluding the Tsushima Islands. Additionally, we confirmed genetic structure of the C. incana population in these areas by using chloroplast DNA sequence analysis to study the intraspecific phylogenetic relationship of C. incana in Japan. We confirmed 37 natural populations in 257 locations throughout West Kyushu excluding the 72 natural populations in the Tsushima Islands. We also confirmed a recent decreasing trend in the number of natural populations in the Nagasaki Mainland. Using the leaves of individuals cultivated from seeds collected from each natural population, we analyzed the chloroplast DNA sequence variations. Among the investigated populations, sequence variations were confirmed in six regions of chloroplast DNA, and those haplotypes were mainly classified into two groups distributed in different areas on the phylogenetic tree. This finding revealed that the common ancestor of C. incana in Japan diverged early into two groups, followed by a fragmentation in population distribution for each area. The haplotype network almost reflected the geographical distribution on haplotypes. However, several haplotypes that were distributed in other areas were confirmed in the Nagasaki Mainland, suggesting a complicated distribution formation in the past.

An expanded phylogeny of the Dennstaedtiaceae ferns: Oenotrichia falls within a non-monophyletic Dennstaedtia, and Saccoloma is polyphyletic

Recent studies have transferred several species previously attributed to the fern genus Oenotrichia to other genera, and even out of the Dennstaedtiaceae to other families. However, the relationship of the type species, O. maxima from New Caledonia, has not previously been investigated using DNA sequences. With phylogenetic analyses of chloroplast DNA sequences, we verify the placement of Oenotrichia within the Dennstaedtiaceae. Moreover, O. maxima actually nests along with Leptolepia in a clade of Dennstaedtia. Dennstaedtia itself is non-monophyletic, with a second clade being more closely related to Microlepia. We outline what is required to resolve the generic taxonomy of this group. We also find that samples attributed to Saccoloma are polyphyletic, with some falling inside the Dennstaedtiaceae and others outside.

Chloroplast DNA sequences support the transfer of the New Caledonian endemic fern Sphenomeris alutacea to Odontosoria

In a recent revision of generic circumscriptions in the Lindsaeaceae ferns, three of the four New Caledonian species previously placed in Sphenomeris were transferred to Odontosoria. Using phylogenetic analyses of chloroplast DNA sequences, we show that the fourth species, Sphenomeris alutacea (Mett.) Copel., also fits within this expanded Odontosoria. Accordingly, we provide a new combination, Odontosoria alutacea (Mett.) Perrie & L.D. Sheph.

Morphological and Molecular Data Support a New Combination in the Neotropical Complex of Cucullate-leaved Species of <I>Syntrichia</I> (Pottiaceae)

Abstract Based on morphological and molecular evidence, a new combination, Syntrichia kingii, is proposed for Tortula kingii, an Andean taxon previously treated as conspecific with S. percarnosa. Tortula nigra is also synonymized with S. kingii. Maximum parsimony and Bayesian analyses of chloroplast DNA sequences (trnL-trnF and trnG regions) were undertaken to assess the affinities between these cucullate-leaved species. Syntrichia kingii is described, illustrated, and its distribution mapped. The known range of this species is extended in the Neotropics to Guatemala, Mexico, and Venezuela. Diagnostic characters, microphotographs, and a morphological comparison with S. percarnosa are provided. Syntrichia percarnosa is excluded from the Mexican moss flora.

Hymenophyllum pluviatile, a new and uncommon fern from New Zealand

Hymenophyllum pluviatile is described as a new and uncommon fern endemic to New Zealand. Phylogenetic analyses of chloroplast DNA sequences show that H. pluviatile is distinct from the other New Zealand species in Hymenophyllum subgenus Globosa. Hymenophyllum pluviatile can be distinguished from its closest New Zealand relatives, Hymenophyllum australe and Hymenophyllum flexuosum, by a suite of morphological and ecological characters. It is mostly confined to the west coasts of the North and South Islands, in areas of high rainfall. Known populations are scattered and small, and more surveys are required to set an informed conservation ranking. Additionally, our morphological and molecular analyses indicate that New Zealand plants previously sometimes referred to Hymenophyllum atrovirens are indistinguishable from Australian material of H. australe. We consequently accept the following members of subgenus Globosa in New Zealand: H. australe, H. demissum, H. flexuosum and H. pluviatile.

Single Base Extension and Fourier-Transform Infra-Red Spectroscopy Techniques; Further Approaches in Discriminating Hazelnut-Adulterated Olive Oil

Background:Confirmation of olive oil authenticity and particularly virgin olive oil has a great importance. Several advanced chemical and genetic analyses have been used to monitor especial components; however each has its limitations especially when detecting hazelnut-adulterated olive oil. Objectives:The objective of this research is to assess the presence of trace amount of hazelnut oil in olive oil (less than 10%) by Single Base Extension (SBE) and Fourier Transform InfraRed Spectroscopy (FTIR). Materials and Methods:The study was based on the analysis of chloroplast DNA sequences using SBE to detect Single Base Polymorphism (SNPs) in highly preserved DNA regions among species to differentiate pure and adulterated olive oil by means of two parallel tools; ABI PRISM automatic sequencer and the SNaPshot lit (APPLERA). Fourier -Transform InfraRed technique has been used for FTIR spectrum comparisons of pure olive oil and hazelnut-adulterated one as well. Results:Total DNA was extracted successfully from pure and hazelnut-adulterated olive oil, and it provided properly acceptable amplification with the primers designed on chloroplast region of both species and admixture oil of them in different ratios; 50: 50, 70: 30, and vice versa. However, for lesser than 10% hazelnut oil in olive oil only SBE analysis provided recognizable results. FTIR spectra of oil samples were assessed at frequency regions of 4000 - 700 cm-1. Eight wave numbers (3007, 1373, 1237, 1120, 1098, 1032, 965, and 722 cm-1) out of eleven differentiating ones were selected as candidate wave-numbers to distinguish pure and adulterated olive oil. Conclusions:SBE technique proved to be an effective strategy to verify olive oil authenticity, especially from hazelnut-adulterated olive oil. However, FTIR technique provided trustable results only when higher than 10% hazelnut oil is present in olive oil.

Chloroplast DNA sequences indicate the grammitid ferns (Polypodiaceae) in New Zealand belong to a single clade, Notogrammitis gen. nov.

Eleven species of grammitid ferns have been recognized from New Zealand, in Ctenopteris (one species) and Grammitis (10 species). On account of their morphology, it has previously been hypothesized that these species belong to a single clade. We found this to be supported by phylogenetic analysis of chloroplast DNA sequences, with the species misclassified in their current genera. Consequently, a new genus is described, Notogrammitis, containing a global total of 12 species. The only grammitid species south of 35°30′S worldwide belong to Notogrammitis. Within Notogrammitis, it appears that small-spored species of more benign habitats have originated from within a grade of larger-spored species, generally of colder environments. The chloroplast DNA sequences indicate several cases where the sampled populations may not actually be conspecific: New Zealand and Tasmanian N. billardierei; the circum-Antarctic N. crassior; and the morphologically variable, New Zealand endemic N. ciliata.

Gymnocalycium esperanzae: A Nothospecies?

Gymnocalycium esperanzae Řepka and Kulhânek, has been recently described from the north central part of Argentina. In this paper the phylogenetic position and hybrid origin of this taxon are explored. Plant material of the supposed parental species was included in phylogenetic analyses with other members of three subgenera of the genus. The results of molecular analyses (cpDNA markers trnL-F, matK and AFLP) showed that G. esperanzae is closely related to members of the subgenus Trichomosemineum, especially G. bodenbenderianum and G. quehlianum. The second supposed parental species, G. castellanosii subsp. armillatum, was separated on a different branch in the tree. According to the special features of its seeds, which are similar to those of G. castellanosii, it clearly belongs to the subgenus Scabrosemineum. Also, molecular data were compared with morphological characters of its supposed parental species: G. bodenbenderianum (subgenus Trichomosemineum) and G. castellanosii subsp. armillatum (subgenus Scabrosemineum), which both grow near the locality of G. esperanzae. G. esperanzae has a very particular set of morphological features, some unique, others intermediate or more inclined to G. bodenbenderianum. Chloroplast DNA sequence analysis and AFLP analysis in combination with morphological features of all three species reveal a hypothesis of a hybrid origin of G. esperanzae.

The Evolutionary Root of Flowering Plants

Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here, we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models. Improving the fit between sequence data and substitution model identifies Trithuria, Nymphaeaceae, and Amborella as surviving relatives of the most basal lineage of flowering plants. This finding indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants. [; ; ; ; ; .].