Two lineages of Lemna aequinoctialis (Araceae, Lemnoideae) based on physiology, morphology, and phylogeny

Lemna aequinoctialis Welw. is a widely spread species that has diverse physiological and molecular properties. Flower characteristics are important factors in deducing taxonomical status; however, owing to the rarity of flowering observations in Lemna, studying them has been a prolonged challenge. In this study, physiological and morphological analyses were conducted by inducing flowering, and molecular analysis was done based on the two chloroplast DNA loci (matK, atpF-atpH intergeneric spacer) of L. aequinoctialis sensu Landolt (1986) from 70 strains found in 70 localities in Japan, Korea, Thailand, and the US. In total, 752 flowering fronds from 13 strains were observed based on axenic conditions. Two different trends in flower organ development-protogyny and adichogamy-were detected in these strains. Their physiological traits were divided into two groups, showing different morphological features based on frond thickness, root cap, and anther sizes. Molecular analysis showed two lineages corresponding to two physiological groups. These were identified as L. aequinoctialis sensu Beppu et al. (1985) and L. aoukikusa Beppu et Murata based on the description of the nomenclature of L. aoukikusa. These were concluded as independent taxa and can be treated as different species. Furthermore, the distribution of L. aoukikusa is not only limited to Japan.

Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis

BACKGROUND

The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants.

RESULTS

The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens.

CONCLUSIONS

The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.

DNA barcode identification of cultivated and wild tropical fruit species

With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03848-w.

Evaluation of chloroplast DNA barcoding markers to individualize Papaver somniferum for forensic intelligence purposes

The opium poppy, Papaver somniferum L., is a forensically important plant due to the medicinal and illegal uses for the milky latex stored in the pods. This latex contains the alkaloids morphine, codeine, and thebaine that are used for their analgesic properties and/or for synthesizing other opioids. However, these compounds are highly addictive and have caused a national opioid epidemic. Two other Papaver species, P. setigerum DC. and P. bracteatum Lindl., are also of forensic interest because they pose both forensic and legal issues. They are largely uncontrolled under the Controlled Substances Act, making these species a common defense strategy. Current morphological and chemical identification methods have been moderately successful but have drawbacks. There is also a lack of sequencing data available. Therefore, exploiting the genome using chloroplast DNA barcoding markers could help to accurately identify these species of interest when plant material is taken. This study screened and assessed the genetic variation both between species and within populations of P. somniferum in nine cpDNA barcode regions (ndhF-rpl32, petA-psbJ, rpl32-trnL, rps16-trnQ, trnE-trnT, trnH-psbA, trnL-trnF, rpl16 intron, and psbE-petL). Published reference genomes from the NCBI GenBank database were aligned and compared for an initial in silico screening. Additionally, ten P. somniferum seed samples from various vendors were sequenced and compared across samples and to published reference data at the various barcode regions of interest. This study showed that the regions trnH-psbA and petA-psbJ have promise for utility in individualization for both inter- and intra-species individualization of P. somniferum.

DNA Isolation from Cocoa-Derived Products and Cocoa Authentication by TaqMan Real-Time PCR

Cocoa (Theobroma cacao L.) is an international commodity used as an ingredient in the manufacturing of chocolate making its authentication a key issue in the cocoa chain. Various molecular techniques have been increasingly applied for quality requirements. These issues highlight the need for techniques that allow the extraction and detection of cocoa DNA from highly processed cocoa products and chocolate. The applicability of real-time PCR to highly processed cocoa-derived products for authentication purposes depends on the possibility of extracting high-quality and amplifiable DNA and further developing efficient PCR tests. This methodology herein describes the use of a classical CTAB method providing DNA suitable for TaqMan real-time PCR amplification. Real-time PCR is a simple and fast method, with a high potential application in a wide range of food products. The main features of this technique are focused on two DNA targets, one located in the nuclear genome (vicilin-li PCR test) and a second one based on chloroplast DNA (lipids PCR test), which successfully passed the performance criteria considering the specificity, sensitivity, efficiency of amplification, robustness, and applicability in processed cocoa-derived products and chocolate.

Genetic diversity and phylogeographic patterns of the dioecious palm Chamaedorea tepejilote (Arecaceae) in Costa Rica: the role of mountain ranges and possible refugia

Gene flow connects populations and is necessary to sustain effective population sizes, and genetic diversity. In the Lower Central American (LCA) region, the complex topographic and climatic history have produced a wide variety of habitats resulting in high biodiversity. Phylogeographic studies of plants from this area are scarce, and to date none have been conducted on palms. We used SSR and chloroplast DNA (cpDNA) markers to study the genetic diversity and structure of populations of the understory palm Chamaedorea tepejilote in Costa Rica. We found that populations of C. tepejilote have moderate to high nuclear simple sequence repeat (SSR) genetic diversity, likely due to large population sizes and its outcrossing mating system. Habitat loss and fragmentation may have contributed to increased genetic structure within slopes. High-elevation mountain ranges appeared to be a significant barrier for gene flow among populations in the Caribbean and Pacific slopes; however, ranges are permeable through low-elevation passes. In contrast, most populations had a single distinct cpDNA haplotype, supporting the hypothesis of several isolated populations that experienced decline that likely resulted in eroded cytoplasmic genetic diversity within populations. The haplotype network and Bayesian analysis linked populations in the Caribbean and the southern Pacific coast, suggesting that gene flow between Pacific and Caribbean populations may have occurred through the southern extreme of the Talamanca Mountain range in Panama, a colonization pathway not previously suggested for LCA plants. This is one of the first phylogeographic studies conducted on tropical palms in the LCA region and the first in the genus Chamaedorea, which sheds light on possible gene flow and dispersal patterns of C. tepejilote in Costa Rica. Our results also highlight the importance of mountain ranges on shaping gene flow patterns of Neotropical plants.

Molecular barcoding of Melissa officinalis L. (badranjboye) in Iran and identification of adulteration in its medicinal services

Medicinal plants are an important source for treatment of diseases in many countries. Today, controlling the quality of the products of medicinal plants is an important task. Customer health may be in danger due to the fraud and misconduct by the sales associates in the sales centers. Melissa officinalis L. (Lamiaceae) is an important medicinal plant used for treatment of several diseases. In Iran, the species of Dracocephalum, Hymencrater, Nepeta and Stachys are mistakenly sold under the name of Badranjboye that have different pharmaceutical properties. For avoiding this mistake, this investigation was performed with the following aims: 1) Checking for the cheating and identifying the Badranjboye in the Iran's market of medicinal plants, 2) Providing the molecular barcode for the medicinal species of Melissa. For this purpose, Market-sold plant samples (leaves) and original reference plant species were compared by morphology, odor as well as Internal transcribed spacer (ITS) and chloroplast DNA ((psbA-trnH) and (trnL-trnF)) sequences. Various molecular analyses, such as sequencing, determination of genetic distance, and construction of phylogenetic tree were performed. These reports have shown that internal transcribed spacer (ITS) and chloroplast DNA (psbA-trnH) sequences are an efficient molecular marker to produce barcode gap and differentiating Melissa officinalis from other species.

Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing

BACKGROUND

Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities.

METHODS

This study reports on the development of a MiSeq FGx® assay targeting seven "hotspot" regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods.

RESULTS

A total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay.

CONCLUSION

Future studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.

Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions

BACKGROUND

The genus Erianthus, which belongs to the "Saccharum complex", includes C₄ warm-season grasses. Erianthus species are widely distributed throughout Southeast Asia, East Asia and South Asia. Erianthus arundinaceus (Retz.) Jeswiet is highly adaptable to the environment, has a high percentage of dry matter, and is highly productive. Recently, this species has attracted attention as a novel bioenergy crop and as a breeding material for sugarcane improvement. Such interest in E. arundinaceus has accelerated the collection and conservation of its genetic resources, mainly in Asian countries, and also evaluation of morphological, agricultural, and cytogenetic features in germplasm collections. In Thailand, genetic resources of E. arundinaceus have been collected over the past 20 years and their phenotypic traits have been evaluated. However, the genetic differences and relatedness of the germplasms are not fully understood.

RESULTS

A set of 41 primer pairs for nuclear simple sequence repeats (SSRs) developed from E. arundinaceus were used to assess the genetic diversity of 121 Erianthus germplasms collected in Thailand; of these primer pairs, 28 detected a total of 316 alleles. A Bayesian clustering approach with these alleles classified the accessions into four main groups, generally corresponding to the previous classification based on phenotypic analysis. The results of principal coordinate analysis and phylogenetic analysis of the 121 accessions on the basis of the SSR markers showed the same trend as Bayesian clustering, whereas sequence variations of three non-coding regions of chloroplast DNA revealed eight haplotypes among the accessions. The analysis of genetic structure and phylogenetic relationships, however, found some accessions whose classification contradicted the results of previous phenotypic classification.

CONCLUSIONS

The molecular approach used in this study characterized the genetic diversity and relatedness of Erianthus germplasms collected across Thailand. This knowledge would allow efficient maintenance and conservation of the genetic resources of this grass and would help to use Erianthus species as breeding materials for development of novel bioenergy crops and sugarcane improvement.

Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups

The influence of neighboring base composition, or context, on substitution bias at fourfold degenerate coding sites and in intergenic regions in plastid DNA is compared across the angiosperms, gymnosperms, ferns, liverworts, chlorophytes, stramenopiles and rhodophytes. An influence of flanking base G + C content on the relative rates of transitions and transversions is observed in all lineages and extends up to four nucleotides from the site of substitution in some. Despite finding context effects in all lineages, significant differences were observed between lineages. Overall, the data suggest that context is a general factor affecting mutation bias in plastid DNA but that the dynamics of the influence have evolved over time. It is also shown that, although there are similar effects of context on substitution bias at fourfold degenerate coding sites and at sites within intergenic regions, there are also small but significant differences, suggesting that there could be some selection on some of these sites and that there could be some difference in the mutation and/or repair process between coding and noncoding DNA.

DNA databases of a CITES listed species Aquilaria malaccensis (Thymelaeaceae) as the tracking tools for forensic identification and chain of custody certification

Aquilaria malaccensis (Thymelaeaceae) is the main source of high-grade agarwood in Southeast Asia. Aggressive collections and trade activities over the past decades have put great pressure on the natural stands and raised concerns over the long-term survival potential of A. malaccensis. Tracking and authentication of agarwood require method with a high degree of accuracy. Therefore, this study aimed to develop DNA databases of A. malaccensis as the tracking tools at species, population and individual levels for forensic identification and chain of custody certification. Using two cpDNA (rbcL and matK) and an rDNA (ITS2) markers, species identification database of Aquilaria was developed to distinguish A. malaccensis from A. hirta, A. microcarpa, A. beccariana, A. crassna, A. sinensis and A. rostrata. In addition, based on 35 populations of A. malaccensis throughout Peninsular Malaysia, cpDNA haplotype and STR allele frequency databases were developed for population and individual identification. A haplotype distribution map based on 29 haplotypes derived from seven cpDNA showed that the A. malaccensis in Peninsular Malaysia can be associated to Kedah-Perak and Kelantan-Johor regions. Similarly, genetic relatedness and Bayesian clustering analyses based on 10 STR markers also divided the 35 populations into two main genetic clusters, corresponding to Kedah-Perak and Kelantan-Johor regions. The STR allele frequency databases were established and characterized according to these two regions. To determine the performance of the STR allele frequency databases for population identification, independent self-assignment tests showed that the percentage of individuals correctly assigned into the origin population was 93.88% in Kedah-Perak and 90.29% in Kelantan-Johor. For the STR allele frequency databases to be used for individual identification, conservativeness tests showed that the θ should be adjusted to 0.250 and 0.200 in the Kedah-Perak and Kelantan-Johor databases, respectively. To ensure consistency in allele calling for the dinucleotide repeat loci across different electrophoretic platforms or laboratories, allelic ladders have been developed for the 10 STR loci. Two case studies are presented of how these databases were used to track A. malaccensis to the origin population and stump. These databases are ready to be used to provide admissible forensic evidence for legal proceedings against the illegal harvesters of agarwood and for agarwood certification to meet the consumer country regulations.

Repairing TALEN-mediated double-strand break by microhomology-mediated recombination in tobacco plastids generates abundant subgenomic DNA

Transcription activator-like effector nuclease (TALEN) technology has been widely used to edit nuclear genomes in plants but rarely for editing organellar genomes. In addition, ciprofloxacin, commonly used to cause the double-strand break of organellar DNA for studying the repair mechanism in plants, confers no organellar selectivity and site-specificity. To demonstrate the feasibility of TALEN-mediated chloroplast DNA editing and to use it for studying the repair mechanism in plastids, we developed a TALEN-mediated editing technology fused with chloroplast transit peptide (cpTALEN) to site-specifically edit the rpoB gene via Agrobacteria-mediated transformation of tobacco leaf. Transgenic plants showed various degrees of chlorotic phenotype. Repairing damaged plastid DNA resulted in point mutation, large deletion and small inversion surrounding the rpoB gene by homologous recombination and/or microhomology-mediated recombination. In an albino line, microhomology-mediated recombination via a pair of 12-bp direct repeats between rpoC2 and ycf2 genes generated the chimeric ycf2-rpoC2 subgenome, with the level about 3- to 5-fold higher for subgenomic DNA than ycf2. Additionally, the expression of chimeric ycf2-rpoC2 transcripts versus ycf2 mRNA agreed well with the level of corresponding DNA. The ycf2-rpoC2 subgenomic DNA might independently and preferentially replicate in plastids.

Technical note: Polyvinylpyrrolidone (PVP) and proteinase-K improve the efficiency of DNA extraction from Japanese larch wood and PCR success rate

Illegal distribution of timber disrupts the timber market and depletes forest resources. DNA markers are used to verify the legal distribution of wood. However, it is difficult to obtain the quantity and quality of DNA suitable for genetic analysis because of the physicochemical properties of wood; therefore, an efficient wood DNA extraction method is required. In this study, to prepare an efficient DNA extraction method from Japanese larch (Larix kaempferi) wood, we investigated the ability of polyvinylpyrrolidone (PVP) and proteinase-K to improve DNA extraction efficiency and PCR success rate. It was found that the addition of PVP resulted in a significant increase in the DNA concentration of the treatment group compared to that of the control group, while the purity (A260/A280) showed no difference. Moreover, the addition of proteinase-K significantly increased both the DNA concentration and purity of the treatment group compared to those of the control group. Further analysis showed that the PCR success rate of psbC (approximately 350 bp) was higher than 90% in the control, PVP treatment, and proteinase-K treatment groups. However, in the PCR success rate of rbcL (approximately 1.3 kb) was higher in the proteinase-K and PVP treatment groups than in the control group. The addition of PVP and proteinase-K increased the success rate of PCR amplification for long regions by preventing DNA damage caused by phenolic compounds and proteins in the wood. The results of this study can thus develop DNA extraction methods to identify the species and origin of woods.

Evaluation of the trnK-matK-trnK, ycf3, and accD-psal chloroplast regions to differentiate crop type and biogeographical origin of Cannabis sativa

Cannabis sativa (marijuana and hemp) is one of the most controversial crops worldwide. In the USA, the state-specific legalization of marijuana and recently legalized hemp pose a problem for law enforcement. This study seeks to utilize chloroplast hSTRs, INDEL, and SNPs markers to develop genotyping methods to aid in the differentiation of legal hemp from illicit marijuana and also for tracking the flow of trafficked marijuana. Three polymorphic regions: trnK-matK-trnK, ycf3, and accD-psal, of the C. sativa chloroplast genome were evaluated in order to distinguish crop type and biogeographic origin. A total of nine polymorphic sites were genotyped from five distinct populations (hemp from the USA and Canada, marijuana from Chile and USA-Mexico, and medical marijuana from Chile) with a custom fragment and SNaPshot^TM assay. The study also combined genotype results from the same sample set using 21 additional polymorphic markers from previous studies. The effectiveness of these multi-locus assays to distinguish sample groups was assessed using haplotype analysis, phylogenetic analysis, pairwise comparisons, and principal component analysis. Results indicated a clear separation of Canadian hemp using only the nine polymorphic sites developed in this study. The additional 21 markers were able to separate US hemp from both marijuana groups to a significant level (p < 0.05) when assessing average Fixation Indices (F_ST). This study demonstrated the applicability of these organelle markers for the determination of crop type and biogeographic origin of C. sativa. However, a more extensive database is needed to evaluate the true discriminatory power of these markers.

Guidelines for the Choice of Sequences for Molecular Plant Taxonomy

This chapter presents an overview of the major plant DNA sequences and molecular methods available for plant taxonomy. Guidelines are provided for the choice of sequences and methods to be used, based on the DNA compartment (nuclear, chloroplastic, mitochondrial), evolutionary mechanisms, and the level of taxonomic differentiation of the plants under survey.

Iris sanguinea is conspecific with I. sibirica (Iridaceae) according to morphology and plastid DNA sequence data

A taxonomic revision of Iris subser. Sibiricae is provided based on morphological and molecular analyses and the study of protologues and original material. Two to three species have been recognized in this subseries by botanists. To address the question of species delimitations and relationships within this group, we analyzed four non-coding regions of plastid DNA (trnS–trnG, trnL–trnF, rps4–trnS^GGA, and psbA–trnH) for samples from 26 localities across the distribution ranges of two currently recognized species, I. sanguinea and I. sibirica. Variance analysis, based on nine characters, revealed no separation between taxa. Moreover, no morphological character could be used to define clear boundaries between taxa. Our results strongly support that I. subser. Sibiricae is monotypic and comprises only I. sibirica, instead of two or three species. Iris sibirica is morphologically variable and one of the most widespread Eurasian species of Iridaceae. Previously accepted taxa, I. sanguinea and I. typhifolia, are synonymised with I. sibirica and also two names, I. orientalis and I. sibirica var. haematophylla, which are typified here, are placed in the synonymy of I. sibirica. Information on the distribution of I. sibirica and the main features used to distinguish between I. sibirica and I. subser. Chrysographes species are provided.

Molecular and morphological discrimination of Chrysanthemum indicum using allele-specific PCR and T-shaped trichome

Chrysanthemum indicum L. is a traditional oriental medicinal herb prepared as a tea from flowers that have been used in China and South Korea since ancient times. It has a long history in the treatment of hypertension, inflammation, and respiratory diseases. Among Chrysanthemum species, C. indicum has more active chemical components as well as better therapeutic effects, and C. indicum is mostly used for medicinal purposes in South Korea. However, the usage of C. indicum has become problematic over the years due to the abundance of adulterated Chrysanthemum and confusion with morphologically related species such as C. morifolium, C. boreale, and Aster spathulifolius. Thus, here we developed a method for molecular authentication using chloroplast universal region rpoC2 and morphological authentication based on T-shaped trichomes of the adaxial leaf surface. By using a species-specific primer derived from the rpoC2 region, we established a multiplex allele-specific PCR for the discrimination of C. indicum. Amplicons of 675 bp for C. indicum and 1026 bp for other Chrysanthemum species were produced using both rpoC2-specific and common primers. These primers can be used to analyze dried samples of Chrysanthemum. Morphological discrimination was performed using T-shaped trichomes present only on the adaxial leaf surface of C. indicum species, and then molecular markers were utilized to authenticate C. indicum products from adulterant samples available in the market. Our results indicate that these molecular markers in combination with morphological differentiation can serve as an effective tool for identifying C. indicum.

Investigation of chloroplast regions rps16 and clpP for determination of Cannabis sativa crop type and biogeographical origin

Cannabis sativa can be classified as either hemp (a legal crop containing less than 0.3% delta-9-tetrahydrocannabinol, THC) or marijuana (an illegal drug containing more than 0.3% THC). Despite its legalization in 33 states for medicinal or recreational use, marijuana remains the most commonly used illicit drug in the USA, and it is heavily trafficked into and within the country. Discriminating between marijuana and hemp is critical to the legal process. Genetic analysis provides a means of analyzing samples unsuitable for chemical analysis, and in addition to discriminating between crop types, DNA may be able to determine the biogeographical origin of samples. In addition, the sharing of rare haplotypes between different seizures may be useful for linking cases and providing investigative leads to law enforcement. This study evaluates the potential of two highly polymorphic regions of the chloroplast genome of C. sativa, rps16 and clpP, to be used for determination of crop type and biogeographical origin. Custom fragment analysis and SNaPshot™ assays were developed to genotype nine polymorphic loci in hemp samples from the USA and Canada, marijuana samples from USA-Mexico and Chile, and medical marijuana samples from Chile. Haplotype analysis revealed eight haplotypes. Only Canadian hemp could be completely differentiated from the other sample groups by haplotype. Phylogenetic analysis and principal component analysis suggested a closer relationship among USA-Mexico marijuana, Chilean marijuana and medical marijuana, and USA hemp. Genotyping additional polymorphisms in future studies is expected to reveal further differences between these sample groups.

A geographical traceability system for Merbau (Intsia palembanica Miq.), an important timber species from peninsular Malaysia

To inform product users about the origin of timber, the implementation of a traceability system is necessary for the forestry industry. In this study, we developed a comprehensive genetic database for the important tropical timber species Merbau, Intsia palembanica, to trace its geographic origin within peninsular Malaysia. A total of 1373 individual trees representing 39 geographically distinct populations of I. palembanica were sampled throughout peninsular Malaysia. We analyzed the samples using a combination of four chloroplast DNA (cpDNA) markers and 14 short tandem repeat (STR) markers to establish both cpDNA haplotype and STR allele frequency databases. A haplotype map was generated through cpDNA sequencing for population identification, resulting in six unique haplotypes based on 10 informative intraspecifically variable sites. Subsequently, an STR allele frequency database was developed from 14 STRs allowing individual identification. Bayesian cluster analysis divided the individuals into two genetic clusters corresponding to the northern and southern regions of peninsular Malaysia. Tests of conservativeness showed that the databases were conservative after the adjustment of the θ values to 0.2000 and 0.2900 for the northern (f = 0.0163) and southern (f = 0.0285) regions, respectively. Using self-assignment tests, we observed that individuals were correctly assigned to populations at rates of 40.54-94.12% and to the identified regions at rates of 79.80-80.62%. Both the cpDNA and STR markers appear to be useful for tracking Merbau timber originating from peninsular Malaysia. The use of these forensic tools in addition to the existing paper-based timber tracking system will help to verify the legality of the origin of I. palembanica and to combat illegal logging issues associated with the species.

Sustaining Life: Maintaining Chloroplasts and Mitochondria and their Genomes in Plants

Chloroplasts (members of the plastid family) and mitochondria are central to the energy cycles of ecosystems and the biosphere. They both contain DNA, organized into nucleoids, coding for critical genes for photosynthetic and respiratory energy production. This review updates the cellular and molecular biology of how chloroplasts, mitochondria, and their genomes in Angiosperms are maintained; particularly in leaf development and maternal inheritance. Maternal inheritance is the common form of transmission to the next generation. Both organelles cannot be derived de novo. Proplastids during very early leaf development develop into chloroplasts with their characteristic thylakoid structure, with the nucleoids associated with the thylakoids. In cell divisions in the leaf primordia and very early leaf development, mitochondria and plastids are duplicated, their nucleoids replicated and segregated, and the population of mitochondria and plastids segregated to daughter cells using the cytoskeleton. To maintain their nucleoids, mitochondria must undergo fusion as well as fission. Chloroplasts are transmitted to the next generation as proplastids where they are maintained in the egg cell but eliminated from the sperm cells. Mitochondria in the apical meristem undergo massive mitochondrial fusion (MMF) prior to floral induction and subsequent maternal inheritance. MMF also occurs again in early germination. MMF encourages DNA repair and recombination, possibly as part of a quality control in each generation. As a further quality control in both chloroplasts and mitochondria, damaged organelles are removed by autophagy. Following consideration of the above, areas requiring further understanding are highlighted.

Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution

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.

Development of species-specific chloroplast markers for the authentication of Gynostemma pentaphyllum and their distribution in the Korean peninsula

Gynostemma pentaphyllum is a traditional oriental medicinal herb used as tea since ancient time. Among Gynostemma species, G. pentaphyllum has more active chemical components and better therapeutic effect. It is used to cure depression, diabetes, anxiety, hyperlipidemia, fatigue, immunity, cancer, and oxidative stress. Overexploitation of G. pentaphyllum for its medicinal benefits has been on a rise, due to which they are adulterated or mistakenly identified with other members of Gynostemma species. Hence, we used chloroplast universal regions such as ycf3, accD, petD, psbB and their polymorphism to distinguish G. pentaphyllum from other Gynostemma species. By using the species-specific primers derived from the above regions, we established a multiplex allele-specific PCR for the authentication of G. pentaphyllum from other species. Thus the PCR reaction produced unique amplicons of size 244 bp and 438 bp for G. pentaphyllum amplified by the primers flanking ycf3, and accD regions respectively. While a 607 bp, and 787 bp amplicons from the primers targeting psbB, and petD regions distinguished G. longipes, G. burmanicum, and G. pubescens species. Moreover, these primers were successful to analyze the dried tea samples of Gynostemma as well. Thus, the developed molecular markers could authenticate different Gynostemma species as well as its products thereby preventing the mistaken-identity of this medicinal herb.

New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east-west lineage split and genetic mixture within western subtropical China

Background

Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources.

Methods

Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods.

Results

Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage.

Discussion

The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China.

Chemical and genomic diversity of six Lonicera species occurring in Korea

Lonicera spp. (Caprifoliaceae) are important not only as a common medicinal herb in East Asia but also as one of the most problematic invasive species in North America. In the present study, we performed a systemic analysis of genomic and chemical diversity among six Lonicera species occurring in Korea, L. japonica, L. maackii, L. insularis, L. sachalinensis, L. praeflorens, and L. vesicaria, using chloroplast DNA whole genome shotgun (WGS) sequencing and LC-MS analyses. The phylogenetic and phylochemical relationships did not coincide with each other, but partial consistency could be found among them. InDel-based cDNA marker for authentication was developed based on the genome sequences. Flavonoids, iridoids, and organic acids were identified in the LC-MS analyses, and their inter-species distribution and localization were also revealed.

Westwards and northwards dispersal of Triosteum himalayanum (Caprifoliaceae) from the Hengduan Mountains region based on chloroplast DNA phylogeography

The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya–Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics of Triosteum himalayanum (Caprifoliaceae), we sequenced three chloroplast DNA fragments (rbcL-accD, rps15-ycf1, and trnH-psbA) from 238 individuals representing 20 populations. Nineteen haplotypes (H1–H19) were identified based on 23 single-site mutations and eight indels. Most haplotypes were restricted to a single population or neighboring populations. Analysis of molecular variance revealed that variations among populations were much higher than that within populations for the overall gene pool, as well as for the East Himalayan group (EH group) and the North Hengduan group (NHM group), but not for the Hengduan Mountains group (HM group). Ecoregions representing relatively high genetic diversity or high frequencies of private haplotypes were discovered, suggesting that this alpine herbaceous plant underwent enhanced allopatric divergence in isolated and fragmented locations during the Quaternary glaciations. The current phylogeographic structure of T. himalayanum might be due to heterogeneous habitats and Quaternary climatic oscillations. Based on the phylogeographic structure of T. himalayanum populations, the phylogenetic relationship of identified haplotypes and palaeodistributional reconstruction, we postulated both westwards and northwards expansion from the HM group for this species. The westwards dispersal corridor could be long, narrow mountain areas and/or the Yarlung Zangbo Valley, while the northwards movement path could be south–north oriented mountains and low-elevation valleys.

Nuclear, chloroplast, and mitochondrial data of a US cannabis DNA database

As Cannabis sativa (marijuana) is a controlled substance in many parts of the world, the ability to track biogeographical origin of cannabis could provide law enforcement with investigative leads regarding its trade and distribution. Population substructure and inbreeding may cause cannabis plants to become more genetically related. This genetic relatedness can be helpful for intelligence purposes. Analysis of autosomal, chloroplast, and mitochondrial DNA allows for not only prediction of biogeographical origin of a plant but also discrimination between individual plants. A previously validated, 13-autosomal STR multiplex was used to genotype 510 samples. Samples were analyzed from four different sites: 21 seizures at the US-Mexico border, Northeastern Brazil, hemp seeds purchased in the US, and the Araucania area of Chile. In addition, a previously reported multi-loci system was modified and optimized to genotype five chloroplast and two mitochondrial markers. For this purpose, two methods were designed: a homopolymeric STR pentaplex and a SNP triplex with one chloroplast (Cscp001) marker shared by both methods for quality control. For successful mitochondrial and chloroplast typing, a novel real-time PCR quantitation method was developed and validated to accurately estimate the quantity of the chloroplast DNA (cpDNA) using a synthetic DNA standard. Moreover, a sequenced allelic ladder was also designed for accurate genotyping of the homopolymeric STR pentaplex. For autosomal typing, 356 unique profiles were generated from the 425 samples that yielded full STR profiles and 25 identical genotypes within seizures were observed. Phylogenetic analysis and case-to-case pairwise comparisons of 21 seizures at the US-Mexico border, using the Fixation Index (F _ST ) as genetic distance, revealed the genetic association of nine seizures that formed a reference population. For mitochondrial and chloroplast typing, subsampling was performed, and 134 samples were genotyped. Complete haplotypes (STRs and SNPs) were observed for 127 samples. As expected, extensive haplotype sharing was observed; five distinguishable haplotypes were detected. In the reference population, the same haplotype was observed 39 times and two unique haplotypes were also detected. Haplotype sharing was observed between the US border seizures, Brazil, and Chile, while the hemp samples generated a distinct haplotype. Phylogenetic analysis of the four populations was performed, and results revealed that both autosomal and lineage markers could discern population substructure.

Genetic analysis of Japanese and American specimens of Scirpus hattorianus suggests its introduction from North America

Scirpus hattorianus is a possible alien species in Japan, and a clarification of its unclear taxonomy is required to reveal its origin. It is not known whether the plants initially described from Japan represent the same species distributed in North America. To clarify the origin of the species, we attempted to sequence old specimens collected about 80 years ago using newly designed primer pairs specific for short sequences, including the variable sites. Chloroplast sequences of ndhF were compared among Japanese and North American S. hattorianus, and the closely related species, S. atrovirens, S. flaccidifolius, and S. georgianus. We succeeded in sequencing all samples, and two haplotypes were detected in S. hattorianus: one was unique to the species and the other, detected from specimens potentially collected from the same population as the types, was shared by both North American S. hattorianus and two closely related species, S. atrovirens and S. flaccidifolius. Our results suggest that Japanese S. hattorianus is an alien species that was introduced from North America at least twice.

Is Didymosphenia geminata an introduced species in New Zealand? Evidence from trends in water chemistry, and chloroplast DNA

Defining the geographic origins of free‐living aquatic microorganisms can be problematic because many such organisms have ubiquitous distributions, and proving absence from a region is practically impossible. Geographic origins become important if microorganisms have invasive characteristics. The freshwater diatom Didymosphenia geminata is a potentially ubiquitous microorganism for which the recent global expansion of nuisance proliferations has been attributed to environmental change. The changes may include declines in dissolved reactive phosphorus (DRP) to low levels (e.g., <2 mg/m³) and increases in dissolved inorganic nitrogen (DIN) to >10 mg/m³ because both these nutrient conditions are associated with nuisance proliferations of D. geminata. Proliferations of D. geminata have been observed in South Island, New Zealand, since 2004. We aimed to address the ubiquity hypothesis for D. geminata in New Zealand using historical river water nutrient data and new molecular analyses. We used 15 years of data at 77 river sites to assess whether trends in DRP or DIN prior to the spread of D. geminata were consistent with a transition from a rare, undetected, species to a nuisance species. We used new sequences of chloroplast regions to examine the genetic similarity of D. geminata populations from New Zealand and six overseas locations. We found no evidence for declines in DRP concentrations since 1989 that could explain the spread of proliferations since 2004. At some affected sites, lowest DRP occurred before 2004. Trends in DIN also did not indicate enhanced suitability for D. geminata. Lack of diversity in the chloroplast intergenic regions of New Zealand populations and populations from western North America is consistent with recent dispersal to New Zealand. Our analyses did not support the proposal that D. geminata was historically present in New Zealand rivers. These results provide further evidence countering proposals of general ubiquity in freshwater diatoms and indicate that, as assumed in 2004, D. geminata is a recent arrival in New Zealand.

Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences

Plants species in the genus Amorphophallus are of great economic importance, as they are the only plants known to produce glucomannan. Although southwestern China has been recognized as one of the origin centres of Amorphophallus, only a few studies assessing its genetic diversity have been reported. To aid in the utilization and conservation of Amorphophallus species, we evaluated the genetic diversity and phylogenetic relationships among seven edible Amorphophallus species using three chloroplast DNA regions (rbcL, trnL and trnK-matK). The results showed that the genetic diversity at the population level was relatively low, with over half of the populations harbouring only one haplotype. The widely scattered species, A. konjac, had the largest genetic diversity, while the narrow endemic species, A. yuloensis, possessed only one haplotype. Phylogeny analysis identified three well-supported major lineages. Our study suggested that habitat fragmentation might be a driver of the genetic variation patterns within and between populations of Amorphophallus. A conservation strategy consisting of in situ conservation and germplasm collection is recommended.

Effectiveness of the DNA barcoding approach for closely related conifers discrimination: A case study of the Pinus mugo complex

DNA barcoding is a standard and efficient method, frequently used for identification, discrimination and discovery of new species. Although this approach is very useful for classifying the world's biodiversity, little is known about its usefulness in barcoding at lower taxonomic level and its discrimination rate for closely related species, like conifers. In this study, we compared the genetic variation of eight chloroplast DNA barcode regions (matK, rbcL, trnH-psbA, trnL-trnF, rpl20-rps18, trnV, ycf1, ycf2) in 17 conifers - three closely related pines from Pinus mugo complex and 14 more distant conifers representing two genera and four sections of the Pinaceae family. The discrimination rate for a single and for multiple DNA barcode regions analyzed in this study was estimated using the Tree-Building and PWG-Distance methods. The usefulness of the DNA barcoding approach for analyzing and resolving taxonomic inconsistency among closely related and more phylogenetically distant conifers was evaluated and discussed.

INTRASPECIFIC CHLOROPLAST DNA VARIATION AND BIOGEOGRAPHY OF NORTH AMERICAN LIRIODENDRON L. (MAGNOLIACEAE)

Restriction site variation in chloroplast DNA (cpDNA) was surveyed to analyze population dynamics in Liriodendron tulipifera L., a woody angiosperm found in eastern North America. Two cpDNA haplotypes, differing by the presence or absence of five restriction site changes (nucleotide sequence divergence estimated as approximately 0.15%) are geographically structured; 61 widespread populations possess the "northern" haplotype and three isolated populations of central Florida possess the "southern" haplotype. This geographic break in cpDNA distribution corresponds to patterns of geographic distribution revealed by a previous survey of allozyme variation, with the exception that analyses of allozyme data further divided the populations containing the northern cpDNA haplotype into two groups, a widespread upland group and a coastal intermediate group. Analyses of these two independent data sets together support the hypothesis that L. tulipifera survived the glacial advances of the Pleistocene in two distinct refugia, possibly as different taxa, and the intermediate coastal group was putatively formed from recent hybridizations between these entities.

SIX INDEPENDENT LOSSES OF THE CHLOROPLAST DNA rpl2 INTRON IN DICOTYLEDONS: MOLECULAR AND PHYLOGENETIC IMPLICATIONS

Previous studies have shown that in several angiosperms and the liverwort Marchantia the chloroplast gene rpl2, encoding ribosomal protein L2, is interrupted by an intron, but that in spinach (Spinacia oleracea, Caryophyllales) this intron has been lost. We have determined the distribution of the rpl2 intron for 390 species representing 116 angiosperm families. Filter hybridizations reveal that the intron is absent from the chloroplast genomes of all examined families of the Caryophyllales, suggesting that the intron was lost in the common ancestor of the order. Sequencing of the rpl2 gene in five genera of the Caryophyllales and in Rumex (Polygonales) not only confirms the filter hybridization results, but also shows that for all taxa lacking the intron, the rpl2 gene has undergone a precise deletion of the intron. In all cases, it is the original rpl2 gene that has sustained loss of its intron. This implies that in chloroplast DNA, integration of exogenous genes (e.g., a reverse transcript of a spliced mRNA) occurs mainly by homologous, replacement recombination, rather than by illegitimate recombination elsewhere in the genome. Filter hybridizations also reveal that the rpl2 intron was lost independently in the common ancestors of at least five other lineages of dicotyledons: Saxifragaceae (s.s.), Convolvulaceae (including Cuscuta), Menyanthaceae, two genera of Geraniaceae, and one genus of Droseraceae. The molecular and phylogenetic implications of these independent intron losses are discussed.

Probing the nucleotide-binding activity of a redox sensor: two-component regulatory control in chloroplasts

Two-component signal transduction systems mediate adaptation to environmental changes in bacteria, plants, fungi, and protists. Each two-component system consists of a sensor histidine kinase and a response regulator. Chloroplast sensor kinase (CSK) is a modified sensor histidine kinase found in chloroplasts-photosynthetic organelles of plants and algae. CSK regulates the transcription of chloroplast genes in response to changes in photosynthetic electron transport. In this study, the full-length and truncated forms of Arabidopsis CSK proteins were overexpressed and purified in order to characterise their kinase and redox sensing activities. Our results show that CSK contains a modified kinase catalytic domain that binds ATP with high affinity and forms a quinone adduct that may confer redox sensing activity.

Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA

The present study describes plastid DNA polymorphism and reports a comparative analysis of two non-coding cpDNA regions (trnC-trnD and atpB-rbcL) in pistachio. Seventeen different genotypes of domestic and wild pistachio from Iran, Syria, Turkey and America were sampled. Total genomic DNA was extracted and amplified with trnC-trnD and atpB-rbcL specific primers and then were sequenced. Phylogenetic relationships and depiction of phylogenetic trees were conducted. Cultivated genotypes of Pistacia vera were classified in a group regardless of their geographic location. P. vera was isolated from Sarakhs but they placed in the two close groups. Among cultivated genotypes, Jalab was separated from other cultivated genotypes. Pistacia Khinjuk was classified with Pistacia atlantica subsp. mutica. The findings confirm the common splitting hypothesis for commercial pistachio genotypes of the P. vera wild-type and also indicated the direct impact of Iranian genotypes in the evolutionary process of cultivated pistachios in other parts of the world. In conclusion it can be inferred that cultivated varieties of pistachio and P. vera var. sarakhs have the same origin, moreover genomic chloroplast could appropriately identify the interspecies relationships of pistachios.

Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA

Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (F_ST = 0) and SAMOVA (F_ST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding.

Complete chloroplast genomes of Aegilops tauschii Coss. and Ae. cylindrica Host sheds light on plasmon D evolution

Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops.

The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication

The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5'-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals.

High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence

BACKGROUND AND AIMS

Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations.

METHODS

Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods.

KEY RESULTS

Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = -0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted.

CONCLUSIONS

It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria.

Evolving California genotypes of Avena barbata are derived from multiple introductions but still maintain substantial population structure

Multiple introductions are thought to enhance the chance of successful colonization, in part because recombination may generate adaptive variation to a new environment. Avena barbata (slender wild oat) is a successful colonist in California, historically noted for striking genetic divergence into two multilocus genotypes, but is still undergoing adaptive change. We sought to understand whether multiple introductions might be contributing to this change. We used cpDNA phylogeography of A. barbata within its home range and in its invaded range in California to determine the minimum number of separate introductions, and the spatial distribution of these introduced lineages. We collected from sites throughout the state of California, where it is an invasive species. Accessions from a representative portion of A. barbata’s full native range were obtained from germplasm repositories. We sequenced seven intergenic chloroplast DNA loci for A. barbata individuals both in California (novel geographic range) and its ancestral range. 204 individuals were assayed for chloroplast haplotype within California using single strand conformational polymorphism SSCPs. Genome size was determined by flow cytometry. Californian accessions are tetraploid as expected, but their genome sizes were smaller than the Old World accessions. There were three haplotypes present in California that were identical to haplotypes in the native range. Within California, the presence of multiple haplotypes at a site was observed primarily in Northern and Central populations. Between populations there was still substantial structure with F_ST ∼ 0.33, due to a shallow latitudinal cline caused by a preponderance of xeric haplotypes in Southern California. There was a minimum of three seed introductions to California. Recombination is thus likely to occur, and contribute to adaptation in new range in this highly-selfing, invader.

Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): molecular evolution of tandemly repeated structural mutations

Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5'-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3' of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3' and 5' acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.

Large-scale asymmetric introgression of cytoplasmic DNA reveals Holocene range displacement in a North American boreal pine complex

Jack pine (Pinus banksiana) and lodgepole pine (Pinus contorta var. latifolia) are two North American boreal hard pines that hybridize in their zone of contact in western Canada. The main objective of this study was to characterize their patterns of introgression resulting from past and recent gene flow, using cytoplasmic markers having maternal or paternal inheritance. Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) diversity was assessed in allopatric populations of each species and in stands from the current zone of contact containing morphological hybrids. Cluster analyses were used to identify genetic discontinuities among groups of populations. A canonical analysis was also conducted to detect putative associations among cytoplasmic DNA variation, tree morphology, and site ecological features. MtDNA introgression was extensive and asymmetric: it was detected in P. banksiana populations from the hybrid zone and from allopatric areas, but not in P. contorta populations. Very weak cpDNA introgression was observed, and only in P. banksiana populations. The mtDNA introgression pattern indicated that central Canada was first colonized by migrants from a P. contorta glacial population located west of the Rocky Mountains, before being replaced by P. banksiana migrating westward during the Holocene. In contrast, extensive pollen gene flow would have erased the cpDNA traces of this ancient presence of P. contorta. Additional evidence for this process was provided by the results of canonical analysis, which indicated that the current cpDNA background of trees reflected recent pollen gene flow from the surrounding dominant species rather than historical events that took place during the postglacial colonization.

Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants

Legumes considered as one of the most important crops worldwide. Due to high price as a PDO product, commercial products of "Fava Santorinis" are often subjected to adulterations from other legume products coming from other Lathyrus or Vicia and Pisum species. Using plant DNA barcoding regions (trnL and rpoC) coupled with High Resolution Melting (Bar-HRM) we have developed a method allowing us to detect and authenticate PDO "Fava Santorinis". Bar-HRM proved to be a very sensitive tool able to genotype Lathyrus and its closed relative species and to detect admixtures, being sensitive enough to as low as 1:100 of non-"Fava Santorinis" in "Fava Santorinis" commercial products. In conclusion, Bar-HRM analysis can be a faster, with higher resolution and cost effectiveness alternative method to authenticate PDO "Fava Santorinis" and to quantitatively detect adulterations in "Fava Santorinis" with other relative commercial "Fava" food products.

Induction of lincomycin and streptomycin resistance by nitrosomethylurea and ethyl methanesulphonate in Capsicum annuum L

A high frequency of plastid-encoded antibiotic-resistant variants of Capsicum annuum were isolated on selective media following treatment by ethyl methanesulphonate (EMS) and nitrosomethylurea (NMU). Seeds and explants were mutagenized with 0.1% EMS and 5 mM NMU separately. Non-mutagenized cotyledons (controls), mutagenized cotyledons from EMS-treated seedlings and NMU-treated cotyledons were placed on regeneration medium supplemented with the antibiotics streptomycin or lincomycin. Resistant shoots appeared at a high frequency in mutagenized cotyledons, whereas in controls morphogenesis was suppressed, accompanied by bleaching. The stability of streptomycin and lincomycin resistance was confirmed by leaf assay. NMU-treated cotyledons gave a higher frequency of variants than cotyledons from EMS-treated seedlings. The mutagenic effect of EMS was more pronounced using whole seeds rather than cotyledons; in contrast, NMU was more effective in inducing variations in cotyledons than in seeds.