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1.
Zhongguo Zhong Yao Za Zhi ; 45(6): 1342-1349, 2020 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-32281346

RESUMO

The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.


Assuntos
DNA de Cloroplastos/genética , Mutação INDEL , Panax notoginseng/genética , Polimorfismo de Nucleotídeo Único , Marcadores Genéticos , Genética Populacional , Alinhamento de Sequência
2.
Mol Phylogenet Evol ; 143: 106665, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31704235

RESUMO

The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia. The phylogenetic relationships are still unclear, especially the delimitation of the genus Microsorum which has been recognized to be non-monophyletic. We analysed the microsoroid ferns using six chloroplast DNA regions (rbcL, rps4+rps4-trnS, trnL+trnL-trnF, atpA, atpB and matK) in order to present a robust hypothesis of their phylogeny. Our results suggest that they comprise up to 17 genera; of them, 12 agree with a previously accepted generic classification. Five tribes are proposed based on the phylogenetic relationships. Most of the species traditionally included in the genus Microsorum are found in six genera belonging to two tribes. In addition to the commonly used DNA markers, the additional atpA and matK are helpful to provide information about the phylogenetic relationships of the microsoroid ferns.


Assuntos
DNA de Cloroplastos , Polypodiaceae/classificação , Marcadores Genéticos , Filogenia , Polypodiaceae/genética
3.
Gene ; 726: 144154, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-31589962

RESUMO

In this work the complete chloroplast DNAs of Allium paradoxum and Allium ursinum, two edible species of Allium subg. Amerallium (the first lineage), were sequenced, assembled, annotated, and compared with complete Allium plastomes of the second and third evolutionary lines from GenBank database. The A. ursinum plastome contains 90 predicted genes (81 unique) including 5 pseudogenes, while A. paradoxum has 88 predicted genes (79 unique) including 19 pseudogenes. The comparative analysis has revealed that the A. paradoxum plastome differs markedly from those of other species. Due to many deletions, the A. paradoxum plastome is the shortest of known for Allium species, being only 145,819 bp long. The most prominent distinctions are (1) a 4825 bp long local inversion that spans from the ndhE to the rpl32 gene in the small single copy region and (2) pseudogenization, or the loss of all NADH-genes. In contrast, the plastome of A. ursinum - a species from the first evolutionary line (as well as A. paradoxum) - resembles the Allium species of the second and third evolutionary lines, showing no large rearrangements or discrepancies in gene content. It is unclear yet whether only A. paradoxum was affected by some evolutionary events or its close relatives from both sect. Briseis and other sections of Amerallium were altered as well. We speculate the sunlight-intolerant, shade-loving nature of A. paradoxum and the impairment of the ndh genes in its plastome could be interrelated phenomena.


Assuntos
Allium/genética , Rearranjo Gênico/genética , Genes de Plantas/genética , Cebolas/genética , DNA de Cloroplastos/genética , DNA de Plantas/genética , Evolução Molecular , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Filogenia , Folhas de Planta/genética , Pseudogenes/genética , Análise de Sequência de DNA/métodos
4.
Int J Mol Sci ; 20(24)2019 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-31817365

RESUMO

Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.


Assuntos
DNA de Cloroplastos/genética , Evolução Molecular , Genoma de Cloroplastos , Lamiales/genética , Fotossíntese/genética , Edição de RNA
5.
PLoS One ; 14(12): e0226985, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31869386

RESUMO

In this study, possible hybridization between two allopatric species, Cornus controversa and Cornus alternifolia, was explored using molecular and morphological approaches. Scanning electron microscope analyses of the adaxial and the abaxial leaf surfaces yielded a few new not yet described characters typical for the particular species and intermediate for hybrids. With the use of 14 Random Amplified Polymorphic DNA and 5 Amplified Fragment Length Polymorphism primer combinations, 44 fragments species specific to C. controversa and 51 species specific to C. alternifolia were obtained. Most of these bands were also found in putative hybrids. All clustering analyses based on binary data combined from both methods confirmed a separate and intermediate status of the hybrids. Hybrid index estimates for hybrids C1-C5 indicated that all were the first generation of offspring (F1). Chloroplast intergenic spacers (trnF-trnL and psbC-trnS) were used to infer the hybridization direction. Based on the assumption of maternal inheritance of chloroplast DNA, C. controversa seems to be the maternal parent of the hybrid. Internal transcribed spacer sequences of the five hybrids analyzed here indicated higher similarity with the sequences of C. controversa (all shared the majority of its single nucleotide polymorphisms). Sequence analysis of PI-like genes fully confirmed the hybrid origin of C1-C5 hybrids. Our results also showed that two specimens in the C. alternifolia group, A1 and A3, are not free of introgression. They are probably repeated backcrosses toward C. alternifolia. Furthermore, molecular data seem to point not only to unidirectional introgression toward C. controversa (the presence of hybrids) but to bidirectional introgression as well, since the presence of markers specific for C. controversa in the profiles of C. alternifolia specimen A3 was observed.


Assuntos
Cornus/genética , Hibridização Genética , Folhas de Planta/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Cornus/ultraestrutura , DNA de Cloroplastos/genética , Folhas de Planta/ultraestrutura , Técnica de Amplificação ao Acaso de DNA Polimórfico
6.
PLoS One ; 14(11): e0225469, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31765416

RESUMO

Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.


Assuntos
Cloroplastos/genética , Fabaceae/genética , Genoma de Cloroplastos , DNA de Cloroplastos/química , DNA de Cloroplastos/isolamento & purificação , DNA de Cloroplastos/metabolismo , Fabaceae/classificação , Genômica , Repetições de Microssatélites/genética , Filogenia , Análise de Sequência de DNA
7.
Genome Biol Evol ; 11(12): 3372-3381, 2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31750905

RESUMO

The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labor-intensive, and this phenomenon remains understudied. Here, we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms, and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.


Assuntos
Cloroplastos/genética , Embriófitas/genética , Genoma de Cloroplastos/genética , DNA de Cloroplastos/genética , Embriófitas/classificação , Genômica , Haplótipos , Sequências Repetidas Invertidas , Recombinação Genética
8.
An Acad Bras Cienc ; 91(3): e20180494, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31618409

RESUMO

Invasive populations of macrophytes are widely distributed and have been successfully introduced and established in freshwater habitats. Hydrilla verticillata was first recorded in 2005 in the Upper Paraná River floodplain and in 2007 at the Itaipu Reservoir (Brazil-Paraguay border, ca. 300 km downstream from its first record). However, its genetic variability within different sites in South America is unknown. We used nucleotide sequences corresponding to the trnL-trnF fragment cpDNA to genetically characterize populations of H. verticillata in different ecosystems of the Upper Paraná River basin. The results indicated an absence of genetic differentiation within and between populations of the basin, and even individuals collected 600 km apart belonged to the same haplotype. Moreover, H. verticillata populations of the Upper Paraná River basin also matched the dioecious biotype haplotype of the Southern United States and Asia. The identification of this single haplotype suggests that one founder genotype was introduced and established successfully in the Upper Paraná River basin, then, as a consequence of vegetative reproduction and the dispersal of propagules, spread to different habitats. However, firm conclusions about this inference can only be obtained with markers of biparental inheritance.


Assuntos
Ecossistema , Hydrocharitaceae/genética , Rios , Brasil , DNA de Cloroplastos , Variação Genética , Espécies Introduzidas , Análise de Sequência de DNA
9.
Genes (Basel) ; 10(10)2019 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-31581648

RESUMO

Rubus boninensis is a rare endemic species found on the Bonin Islands with a very restricted distribution. It is morphologically most closely related to Rubus trifidus, occurring widely in the southern Korean peninsula and Japan. This species pair provides a good example of anagenetic speciation on an oceanic island in the northwestern Pacific Ocean-R. trifidus as a continental progenitor and R. boninensis as an insular derivative species. In this study, we firstly characterized the complete plastome of R. boninensis and R. trifidus and compared this species pair to another anagenetically derived species pair (R. takesimensis-R. crataegifolius). The complete plastome of R. trifidus was 155,823 base pairs (bp) long, slightly longer (16 bp) than that of R. boninensis (155,807 bp). No structural or content rearrangements were found between the species pair. Eleven hotspot regions, including trnH/psbA, were identified between R. trifidus and R. boninensis. Phylogenetic analysis of 19 representative plastomes within the family Rosaceae suggested sister relationships between R. trifidus and R. boninensis, and between R. crataegifolius and R. takesimensis. The plastome resources generated by the present study will help elucidate plastome evolution and resolve phylogenetic relationships within highly complex and reticulated lineages of the genus Rubus.


Assuntos
Plastídeos/genética , Rubus/classificação , Rubus/genética , DNA de Cloroplastos/genética , DNA de Plantas/genética , Variação Genética/genética , Repetições de Microssatélites/genética , Filogenia , República da Coreia , Análise de Sequência de DNA/métodos
10.
Biomed Res Int ; 2019: 7265030, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31531364

RESUMO

The papilionoid legume genus Ormosia comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five Ormosia species by Illumina sequencing. The Ormosia chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with trnK-rbcL, atpE-trnS-rps4, trnC-petN, trnS-psbZ-trnG, trnP-psaJ-rpl33, and clpP intron being the most variable regions. Phylogenetic analysis revealed that Ormosia is in the Papilionoideae clade and is sister to the Lupinus clade. Overall, this study, which provides Ormosia chloroplast genomic resources and a comparative analysis of Ormosia chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Ormosia and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.


Assuntos
Cloroplastos/genética , Fabaceae/genética , Genoma de Cloroplastos/genética , Mutação/genética , Austrália , DNA de Cloroplastos/genética , Evolução Molecular , Extremo Oriente , Genética Populacional/métodos , Genômica/métodos , Repetições de Microssatélites/genética , Filogenia , Análise de Sequência de DNA/métodos
11.
PLoS One ; 14(9): e0222707, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31536553

RESUMO

To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius. We broadly sampled a total of 315 accessions in 35 populations and sequenced five noncoding regions of chloroplast DNA. Rubus takesimensis emerged as nonmonophyletic and several geographically diverse continental populations were likely responsible for the origin of R. takesimensis; the majority of R. takesimensis accessions were sisters to the clade containing accessions of R. crataegifolius, primarily from the Korean peninsula, while rare accessions from three populations shared common ancestors with the ones from the southern part of the Korean peninsula, Jeju Island, and Japan. A few accessions from the Chusan population originated independently from the Korean peninsula. Of 129 haplotypes, 81 and 48 were found exclusively in R. crataegifolius and R. takesimensis, respectively. We found unusually high genetic diversity in two regions on Ulleung Island and no geographic population structure. For R. crataegifolius, two major haplotype groups were found; one for the northern mainland Korean peninsula, and the other for the southern Korean peninsula and the Japanese archipelago. Compared with populations of R. crataegifolius sampled from Japan, much higher haplotype diversity was found in populations from the Korean peninsula. The patterns of genetic consequences in R. takesimensis need to be verified for other endemic species based on chloroplast DNA and independent nuclear markers to synthesize emerging patterns of anagenetic speciation on Ulleung Island.


Assuntos
Especiação Genética , Variação Genética , Haplótipos , Rubus/genética , DNA de Cloroplastos/análise , DNA de Cloroplastos/genética , DNA de Plantas/análise , DNA de Plantas/genética , Genética Populacional , Geografia , Ilhas , Japão , Filogenia , República da Coreia , Rubus/classificação , Rubus/crescimento & desenvolvimento , Análise de Sequência de DNA , Especificidade da Espécie
12.
Mol Phylogenet Evol ; 141: 106626, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31526848

RESUMO

Studies about the drivers of angiosperm clade diversifications have revealed how the environment continuously alters the species chances to adapt or to go extinct. This process depends on complex interactions between abiotic and biotic factors, conditioned to the geological and tectonic settings, the genetic variability of species and the rate at which speciation occurs. In this study, we aim to elucidate the timing of diversification of the Lithospermeae, the second largest tribe within Boraginaceae, and to identify the possible morphological and ecological characters associated with shifts in diversification rates of the most species-rich clades. Lithospermeae includes ca. 470 species and 26 genera, among which are some of the largest genera of the family such as Onosma (150 spp.), Echium (60 spp.), and Lithospermum (80 spp.). An exhaustive study of the whole clade is not available to date and its evolutionary history and diversification rates are incompletely known. In the present study, we provide the most comprehensive phylogeny of the group so far, sampling 242 species and all 26 genera. We found that crown-groups and diversification rates of Lithospermeae largely date back to the Mid-Miocene, with high diversification rates in the largest genera, though only significantly high in Onosma. Our analysis fails to associate any of the functional or morphological traits considered with significant shifts in diversification rates. The timing of the diversification of the species-rich clades corresponds with Miocene tectonic events and global climate changes increasing aridity across Eurasia and western North America. These results suggest a causal link between known ecological features of Lithospermeae (i.e., pre-adaptation to arid, open habitats, and mineral soils) and their diversification. Future studies should expand the sampling of individual subclades and detailed functional analyses to identify the contribution of adaptations to arid conditions and pollinator shifts.


Assuntos
Biodiversidade , Boraginaceae/classificação , Filogenia , Filogeografia , Sequência de Bases , Boraginaceae/anatomia & histologia , DNA de Cloroplastos/genética , DNA Espaçador Ribossômico/genética , América do Norte , Especificidade da Espécie , Fatores de Tempo
13.
Genes Genet Syst ; 94(4): 151-158, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31495805

RESUMO

Arabidopsis thaliana, one of the most important model plants, has played an essential role in every biological field including evolutionary biology. Recent population genomic studies have gradually clarified the origin and evolution of this species. Nevertheless, incongruent patterns among gene trees based on cytogenetic data have highlighted the importance of understanding the life history evolution and landscape biogeography of extant A. thaliana populations. Here, we focus on the maternally inherited chloroplast genome in A. thaliana and carry out phylogeographic analyses and coalescent time estimations. The maternal lineage of A. thaliana originated in the European to West and Central Asian regions in the Early Pleistocene. Relicts, the ancient lineages suggested by population genomic data, are not ancestral maternal lineages, but are derived from the European population. Part of the European population then dispersed eastward and spread to the Indian region, and finally extended to the Yangtze River region. The branching patterns and evolutionary time scales of the maternal genealogy are significantly different from those estimated from analyses of autosomal genes, and these cannot be explained by incomplete lineage sorting of the ancestral polymorphisms during the coalescent process due to large differences in the evolutionary time scale involved.


Assuntos
Arabidopsis/genética , Cloroplastos/genética , DNA de Cloroplastos/genética , Evolução Molecular , Variação Genética/genética , Genética Populacional , Herança Materna/genética , Filogeografia , Análise de Sequência de DNA
14.
J Plant Res ; 132(6): 741-758, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31489497

RESUMO

Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers.


Assuntos
Variação Genética , Magnolia/genética , Evolução Biológica , DNA de Cloroplastos/análise , Ecossistema , Magnolia/anatomia & histologia , Magnolia/classificação , Repetições de Microssatélites , Filogenia , Filogeografia , Dispersão Vegetal , Folhas de Planta/anatomia & histologia
15.
Int J Legal Med ; 133(6): 1721-1732, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31444552

RESUMO

Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA. Despite its schedule I classification by the federal government, 33 states and the District of Columbia have legalized its use for medicinal or recreational purposes. This state-specific legalization has created a new problem for law enforcement: preventing and tracking the diversion of legally obtained Cannabis to states where it remains illegal. In addition, trafficking of the drug at the border with Mexico remains an issue for law enforcement agencies. C. sativa crops can be classified as marijuana (a drug containing the psychoactive chemical delta-9-tetrahydrocannabinol) or hemp (the non-drug form of the plant). Differentiation between crop types is important for forensic purposes. In addition, investigation of trafficking routes into and within the USA requires genetic association of samples from different seizures, and determining where the crop originated could provide important leads. This project seeks to exploit sequence variations in C. sativa chloroplast DNA (cpDNA) to allow genetic determination of biogeographic origin, discrimination between marijuana and hemp, and association between cases for C. sativa samples. Due to the limited discriminatory ability of common barcoding markers, the authors sought to discover more informative polymorphic regions. By comparing published whole genome cpDNA sequences, 58 polymorphisms and seven hotspot regions were identified. Hemp samples from the USA and Canada, marijuana samples from Mexico and Chile, and medical marijuana samples from Chile were evaluated using two cpDNA hotspot regions, rpl32-trnL and trnS-trnG. Principal component analysis supported some differences between the groups based on their crop type and biogeographic origin.


Assuntos
Cannabis/genética , DNA de Cloroplastos/genética , Variação Genética , Análise de Sequência de DNA , Bases de Dados Genéticas , Tráfico de Drogas , Genoma de Planta , Genótipo , Haplótipos , Humanos , Filogeografia , Análise de Componente Principal
16.
BMC Plant Biol ; 19(1): 361, 2019 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-31419941

RESUMO

BACKGROUND: The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. RESULTS: A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. CONCLUSIONS: These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.


Assuntos
Asparagus (Planta)/genética , Núcleo Celular/genética , Cromossomos de Plantas/genética , DNA de Cloroplastos/genética , Genoma de Planta/genética , Evolução Biológica , Evolução Molecular
17.
J Plant Res ; 132(5): 589-600, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31385106

RESUMO

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson's sect. Leucantherae and Zhang's sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification.


Assuntos
Eriocaulaceae/classificação , Evolução Molecular , Núcleo Celular/genética , DNA de Cloroplastos/análise , Eriocaulaceae/genética , Filogenia , Análise de Sequência de DNA
18.
PLoS One ; 14(7): e0216966, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31291259

RESUMO

Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.


Assuntos
Larix/genética , Mapeamento Cromossômico , DNA Antigo , DNA de Cloroplastos/genética , DNA Mitocondrial/genética , DNA de Plantas/genética , Variação Genética , Genética Populacional , Genoma de Cloroplastos , Genoma Mitocondrial , Genoma de Planta , Haplótipos , História Antiga , Larix/classificação , Polimorfismo de Nucleotídeo Único , Sibéria , Taiga , Tundra
19.
PLoS One ; 14(7): e0219700, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31299064

RESUMO

The ability to detect founding populations of invasive species or rare species with low number of individuals is important for aquatic ecosystem management. Traditional approaches use historical data, knowledge of the species' ecology and time-consuming surveys. Within the past decade, environmental DNA (eDNA) has emerged as a powerful additional tracking tool. While much work has been done with animals, comparatively very little has been done with aquatic plants. Here we investigated the transportation and seasonal changes in eDNA concentrations for an invasive aquatic species, Elodea canadensis, in Norway. A specific probe assay was developed using chloroplast DNA to study the fate of the targeted eDNA through space and time. The spatial study used a known source of Elodea canadensis within Lake Nordbytjern 400 m away from the lake outlet flowing into the stream Tveia. The rate of disappearance of E. canadensis eDNA was an order of magnitude loss over about 230 m in the lake and 1550 m in the stream. The time series study was performed monthly from May to October in lake Steinsfjorden harbouring E. canadensis, showing that eDNA concentrations varied by up to three orders of magnitude, peaking during fall. In both studies, the presence of suspended clay or turbidity for some samples did not hamper eDNA analysis. This study shows how efficient eDNA tools may be for tracking aquatic plants in the environment and provides key spatial and temporal information on the fate of eDNA.


Assuntos
DNA de Cloroplastos/análise , Monitoramento Ambiental/métodos , Hydrocharitaceae/genética , Espécies Introduzidas , Ecossistema , DNA Ambiental , Geografia , Lagos , Noruega , Rios , Estações do Ano , Análise de Sequência de DNA
20.
PLoS One ; 14(7): e0219070, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31329604

RESUMO

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.


Assuntos
Borboletas/fisiologia , Dieta , Ecossistema , Animais , Formigas/fisiologia , Isótopos de Carbono , Código de Barras de DNA Taxonômico , DNA de Cloroplastos/genética , DNA de Cloroplastos/isolamento & purificação , Fabaceae/química , Fabaceae/genética , Microbioma Gastrointestinal/genética , Herbivoria/genética , Larva/fisiologia , Isótopos de Nitrogênio , Simbiose
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