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373 results for “Chloroplast”
The dataset of five chloroplast regions used in: A contribution to Gymnosphaera (Cyatheaceae) in mainland Asia: Two new species, reinstatement of Cyathea bonii, and their phylogenetic positions
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The data of complete chloroplast genome sequence of Sorbus amabilis (Rosaceae) in China
<p>This dataset includes the complete chloroplast genome of <em>Sorbus amabilis </em> in China.</p>
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
Chloroplast genome of Phyllostachys glauca
<p><span><i>Phyllostachys glauca</i> is a dominant species in limestone mountains endemic to China. Here, we characterized its complete chloroplast genome. It is a circular DNA molecule of 139689 bp in length, including a pair of 21798 bp inverted repeats (IRs), a 12872 bp small single-copy (SSC) region and an 83221 bp large single-copy (LSC) region. The total GC content of <i>P. glauca</i> chloroplast genome was 38.9%, and it encodes a total of 137 functional genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The phylogenetic analysis shows that <i>P. glauca</i> is highly clustered in the <i>Phyllostachys</i> clade (V), sister to the lineage of <i>P. nigra</i> var. <i>henonis</i> + <i>P. sulphurea</i>.</span></p>
Contact zone of two different chloroplast lineages and genetic guidelines for seed transfer in Quercus serrata and Q. crispula
<p>Within their natural distribution ranges, plant species exhibit genetic structure which has been created by global climate change and natural selection over long periods. To conserve local forests with different genetic structures, genetic guidelines for seed and seedling transfer in individual species are therefore necessary. Genetic guidelines have been published for 43 Japanese tree species using population genetic data; however, for practical use, more detailed genetic borders between important genetic lineages should be clarified to inform seed collection and planting. Thus, we investigated in detail the genetic borders between two important Japanese oak species, Quercus serrata and Q. crispula, in the Chubu region of Japan using chloroplast and nuclear DNA markers, and we discuss the factors that influenced border creation using the results of species distribution modelling (SDM). Two distinct cpDNA haplotypes were found for each species (northern and southern haplotype) within the Chubu region of Japan but the difference in nuclear DNA between northern and southern haplotype populations was very small both in Q. serrata and Q. crispula. The results of SDM showed that during the LGM Q. serrata was distributed mostly along the coastline but Q. crispula was distributed not only along the coast but also in mountainous areas further inland. The cpDNA genetic borders of these two oak species are complex and seem to have been influenced by topography and their distribution during the LGM. We propose and discuss genetic guidelines for these two oak species based on the results of this study.</p>
Data from: Chloroplast population genetics reveals low levels of genetic variation and conformation to the central–marginal hypothesis in Taxus wallichiana var. mairei, an endangered conifer endemic to China
The central–marginal hypothesis predicts that geographically peripheral populations should exhibit reduced genetic diversity and increased genetic differentiation than central populations due to smaller effective population size and stronger geographical isolation. We evaluated these predictions in the endangered conifer Taxus wallichiana var. mairei. Eight plastid simple sequence repeats (cpSSRs) were used to investigate plastid genetic variation in 22 populations of Taxus wallichiana var. mairei, encompassing nearly its entire distribution range. Low levels of plastid genetic variation and differentiation were detected in the populations, and the findings were attributed to low mutation rates, small population sizes, habitat fragmentation and isolation, and effective pollen or seed dispersal. Hunan and Hubei were identified as major refugia based on the number of private haplotypes and species distribution modeling. Trends in plastid genetic diversity and genetic differentiation from central to peripheral populations supported the predictions of the central–marginal hypothesis. In scenarios wherein the future climate becomes warmer, we predict that some peripheral populations will disappear and southern and southeastern regions will become significantly less habitable. Factors that include the levels of precipitation during the driest month, annual precipitation level, and annual temperature range will be decisive in shaping the future distribution of these populations. This study provides a theoretical basis for the conservation of T. wallichiana var. mairei.
DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae
<p><span>As an ancient clonal root and leaf crop, taro (<i>Colocasia esculenta</i>) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other <i>Colocasia</i> species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea. </span></p>
Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
<p><span><span><span><span><span><span><span><span><span><span><span>Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridisation and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridisation has previously been reported in the Australian endemic plant genus <i>Adenanthos </i>(Proteaceae). Like many Australian genera, <i>Adenanthos</i> is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for <i>Adenanthos</i>, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridisation and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also result from extensive ancient introgression as well as recent chloroplast capture and introgression between extant <i>Adenanthos </i>species<i>. </i>The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localised populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in <i>Adenanthos</i> coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Data from: Chloroplast phylogenomic data support Paleocene - Eocene amphi-Pacific early radiation for the Asian Palmate core Araliaceae
Traditional phylogenies based on analysis of multiple genes have failed to obtain a well-resolved evolutionary history for the backbone of the Asian Palmate group of Araliaceae, the largest clade of the family. In this study we applied the genome skimming approach of next-generation sequencing to address whether the lack of resolution at the base of the Asian Palmate tree is due to molecular sampling error or the footprint of an ancient radiation. Twenty-nine complete plastid genomes of Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, BioGeoBears) to provide the first phylogenomic reconstruction of the group (95% of genera included). As a result, the early divergences of the Asian Palmate group have been clarified but the backbone of its core is not totally resolved, with short internal branches pointing to an ancient radiation scenario. East Asia is inferred as the most likely ancestral area for the Asian Palmate group (early Upper Cretaceous and the Paleocene) from which an early colonization of the Neotropics is inferred during the late Paleocene – early Eocene. The radiation of the core took place during the Paleocene – early Eocene, most likely in the context of the Boreotropical hypothesis. Recurrent episodes of southward migration (to the tropics) coupled with northern latitude local extinctions (promoting lineages geographic isolation) and northward expansion (promoting lineages contact that erased the trace of preceding geographic isolation) are hypothesized to have linked to the alternation of the cold and warm periods of the Eocene.
Data from: Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers
Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.
Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other's closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.
Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions
The genus Amaranthus (pigweeds) is a group of ∼74 monoecious or dioecious annual species native to every continent but Antarctica, frequently associated with natural and human disturbance, with several economically important domesticated and weedy species. We set out to reconstruct the phylogeny of Amaranthus, with broad geographic sampling, in order to answer questions about biogeographic relationships in the genus and the monophyly of the subgenera. Fifty-eight species were included inmaximum parsimony and Bayesian phylogenetic analyses based on ITS and three low-copy nuclear genes (A36, G3PDH, and Waxy), as well as two chloroplast regions (trnL5′-trnL3′ and matK/trnK). Topology tests were also employed to test taxonomic hypotheses about incongruence between trees and the monophyly of clades containing Galápagos species. Our analyses support the origin of the genus in the Americas, with a single long-distance dispersal event to the Old World, and both nuclear and chloroplast trees recover three to fourmajor clades, roughly corresponding to three subgenera recognized based on morphology. However, there are species in all of these clades that were not predicted based on morphology, and we discover previously unsuspected relationships between Galápagos species and species from the North American Southwest, which comprise small monophyletic groups outside of the three recognized subgenera. Additionally, an important herbicide resistant weed species (A. palmeri) and its sister species are placed into different large clades based on nuclear or chloroplast data, suggesting a chloroplast capture event. These results will provide a basis for further exploration of the evolution of weedy ecological strategies in the group.
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.
Data from: Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces
We analyzed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America super-region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kind of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Meso-America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of germplasm collections.
Data from: Chloroplast DNA-based phylogeography of Tilia americana (Malvaceae)
A comprehensive picture of how plant species and communities move and evolve over time will require that a variety of species be studied, including plants with different life histories, rarity, and distributions. Relatively few phylogeographic studies have focused on trees. In the present study, the phylogeographic history of Tilia americana, American basswood, was investigated. Samples were collected from throughout the United States and Mexican ranges of basswood, and a phylogenetic analysis was conducted based on sequence data from two non-coding chloroplast DNA regions. The results showed no evidence for the various hypotheses of multiple basswood species within the U. S. A., but there is evidence for a divergence between a Mexican and U. S. A. clade within basswood. Population genetics and spatial statistical analyses were also performed, and supported the conclusion that the only significant geographic barrier within the North American basswoods is found between U. S. A. and Mexico. An attempt was also made to interpret the anomalous geographic distribution of certain chloroplast haplotypes, raising further questions about past migration routes of North American temperate forest trees.
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome. in Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan
FIGURE. The Bayesian tree of the Adaintum pedatum complex based on chloroplast markers and corresponding rhizome type. Support values (Bayesian inference posterior probability (BIPP) (upper) ≥ 0.5, and maximum likelihood bootstrap support (MLBS) (nether) ≥ 50%) are shown above the main branches, the thickened branches indicate MLBS=100 and BIPP=1. Yellow bar means erect rhizome; blue bar means creeping rhizome; gray bar means decumbent or short-creeping rhizome.
Drakaea glyptodon nuclear microsatellite and chloroplast haplotype data
<p class="CxSpFirst">Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. <span>Ten</span> populations of the common terrestrial orchid <i>Drakaea glyptodon</i> from Southwest Australia were genotyped with ten nuclear and five chloroplast SSR markers. Levels and partitioning of genetic variation, and effective population sizes (<i>N</i><sub>e</sub>), were estimated. Spatial genetic structure of nuclear diversity, together with chloroplast data, are used to infer the effective number of seed parents per population. We found high genetic diversity, <i>N</i><sub>e</sub> values that generally exceed predictions based on the number of flowering individuals, and moderate levels of gene flow. Two populations were founded by < 5 colonists suggesting some populations are colonized by few seeds, with growth largely resulting from <i>in situ</i> recruitment. A value of 3.65 for <i>m</i><sub>p </sub>/<i>m</i><sub>s</sub> indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that <i>D. glyptodon</i> is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes.</p>
Chloroplast genome of the invasive Pyrus calleryana
<p>The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P.<b> </b>phaeocarpa<b>) </b>read<b> </b>mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy region (SSC; 19.239 bp). In total, 115 unique genes were predicted and annotated in that genome, including 81 protein coding genes, 30 tRNA coding genes, and 4 rRNA coding genes. Phylogenetic analyses based on the whole chloroplast genome sequences places the P. calleryana among other Rosaceae plants, specifically among the Asian species of Pyrus.</p>
Supplementary material 1 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
NCBI accession numbers of DNA barcoding sequences, and complete chloroplast genomes used in this study.
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