A CRISPR-based strategy for targeted sequencing in biodiversity science

Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

First report of Ageratum yellow vein virus infecting papaya in Lampung, Indonesia

BACKGROUND

Papaya (Carica papaya) is a tropical fruit of great economic and nutritional importance, loved for its sweet and delicious flesh. However, papaya cultivation faces serious challenges in the form of Begomovirus attacks. Begomoviruses are a group of viruses that pose a serious threat to plants worldwide. Including papaya, Begomovirus has become a significant threat to papaya production in various parts of the world and has been identified in several regions in Indonesia.

METHODS

DNA was extracted from seven samples representing different papaya growing areas using a Plant Genomic DNA Mini Kit. Genomic DNA from the samples was subjected to PCR using universal primers of AC2, AC1, SPG1 and SPG2. The PCR products then sequenced using the dideoxy (Sanger) approach. The obtained sequence then compared to the gene bank using BLAST software available at NCBI. Multiple sequence alignment and phylogenetic tree construction were analyzed using the MEGA11 program.

RESULTS

Detection based on viral nucleic acid in papaya plants in Pesawaran, Lampung Province with seven sampling points using universal primers SPG1/SPG2 showed positive results for Begomovirus infection with visible DNA bands measuring ± 900 bp. Direct nucleotide sequencing using SPG1/SPG2 primers for the AC2 and AC1 genes of the Begomovirus and confirmed by the BLAST program showed that papaya samples were infected with Ageratum yellow vein virus (AYVV). The phylogenetic results show that AYVV from papaya samples has a close relationship with the AYVV group from several other countries, with 98% homology.

CONCLUSION

In the papaya cultivation area in Pesawaran, Lampung province, it was identified as Begomovirus, Ageratum yellow vein virus (AYVV) species and is closely related to the AYVV group from several other countries. Overall, our study further suggests that Ageratum acts as an alternative host and reservoir for Begomovirus.

Rapid Detection of the Strawberry Foliar Nematode Aphelenchoides fragariae Using Recombinase Polymerase Amplification Assay with Lateral Flow Dipsticks

Rapid and reliable diagnostic methods for plant-parasitic nematodes are critical for facilitating the selection of effective control measures. A diagnostic recombinase polymerase amplification (RPA) assay for Aphelenchoides fragariae using a TwistAmp® Basic Kit (TwistDx, Cambridge, UK) and AmplifyRP® Acceler8® Discovery Kit (Agdia, Elkhart, IN, USA) combined with lateral flow dipsticks (LF) has been developed. In this study, a LF-RPA assay was designed that targets the ITS rRNA gene of A. fragariae. This assay enables the specific detection of A. fragariae from crude nematode extracts without a DNA extraction step, and from DNA extracts of plant tissues infected with this nematode species. The LF-RPA assay showed reliable detection within 18-25 min with a sensitivity of 0.03 nematode per reaction tube for crude nematode extracts or 0.3 nematode per reaction tube using plant DNA extracts from 0.1 g of fresh leaves. The LF-RPA assay was developed and validated with a wide range of nematode and plant samples. Aphelenchoides fragariae was identified from seed samples in California. The LF-RPA assay has great potential for nematode diagnostics in the laboratory with minimal available equipment.

Identifying a suspect powder as a cannabis concentrate through chemical analysis and DNA testing

PURPOSE

Cannabis is regulated in many countries, and cannabis products are diversifying, which can hinder identification. Here, we report the seizure of a powder sample with a cannabis-like odor in a spice bottle labeled "nutmeg" and identification of the sample by chemical testing and cannabis DNA testing.

METHODS

The sample was observed under a microscope, extracted with methanol, and analyzed by gas chromatography-mass spectrometry (GC-MS). The chemical profile of the seized powder was compared with that of nutmeg samples. Gas chromatography-flame ionization detection was used to estimate the total Δ9-tetrahydrocannabinol (Δ9-THC) concentration in the sample. A commercially available cannabis DNA testing kit was used to confirm the presence of cannabis plant DNA in the seized sample.

RESULTS

The characteristics of cannabis in the seized powder were difficult to determine through microscopic observation alone. GC-MS analysis identified β-caryophyllene (an aromatic component of cannabis) and five cannabinoids unique to cannabis, including Δ9-THC. No common compounds were identified in the seized powder or nutmeg samples. The total Δ9-THC concentration in the sample was very high (approximately 47% by weight). Cannabis DNA testing confirmed that the seized powder contained cannabis.

CONCLUSIONS

The seized powder was found to be a processed product made from a finely pulverized resin-like cannabis concentrate. Our results indicate that combined chemical and DNA analysis should help identify cannabis-related samples in various forms.

Function and Characteristic Analysis of Candidate PEAR Proteins in Populus yunnanensis

PEAR proteins are a type of plant-specific DNA binding with one finger (Dof) transcription factors that play a key role in the regulation of plant growth, especially during phloem cell growth and seed germination in Arabidopsis. However, the identification, characteristics and function of PEAR proteins, particularly in woody plants, need to be further studied. In the present study, 43 candidate PEAR proteins harboring the conserved Zf-Dof domain were obtained in Populus yunnanensis. Based on phylogenetic and structural analysis, 10 representative PEAR candidates were selected, belonging to different phylogenetic groups. The functions of PEAR proteins in the stress response, signal transduction, and growth regulation of stem cambium and roots undergoing vigorous cell division in Arabidopsis were revealed based on their expression patterns as characterized by qRT-PCR analysis, in accordance with the results of cis-element analysis. In vitro experiments showed that the interaction of transcription factor (E2F) and cyclin indirectly reflects the growth regulation function of PEAR through light signaling and cell-cycle regulation. Therefore, our results provide new insight into the identity of PEAR proteins and their function in stress resistance and vigorous cell division regulation of tissues in P. yunnanensis, which may serve as a basis for further investigation of the functions and characteristics of PEAR proteins in other plants.

A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens

Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newly described bioinformatic methods have been developed to estimate ploidy levels using high-throughput sequencing data, and these have been optimized in plants by calculating allelic ratio values from target capture data. This method relies on the maintenance of allelic ratios from the genome to the sequence data. For example, diploid organisms will generate allelic data in a 1:1 proportion, with an increasing number of possible allelic ratio combinations occurring in individuals with higher ploidy levels. In this chapter, we explain step-by-step this bioinformatic approach for the estimation of ploidy level.

Tinnea gombea (Lamiaceae), a new species from the Sudanian savanna region, Nigeria based on integrative evidence

Tinnea gombea, endemic to the Sudan savanna grasslands in northern Nigeria, is described and illustrated. We used integrative evidence from morphological characters, ecology and molecular phylogenetic data. The new species is morphologically and ecologically similar to T. barteri and T. aethiopica, but can be readily delimited from these taxa by unique characters including a subshrub growth habit, leaves alternate to subopposite, blades lanceolate, apically acuminate, inflorescences raceme, bearing solitary flowers in upper leaf and bract axils, lilac to purplish dusky flowers and the inflated fruits dehiscent. The distribution and habitat of T. gombea are also distinctive, being restricted to the Sudan savanna, while the two most similar species are widespread in tropical Africa. Additionally, molecular phylogenetic assessments using nrITS and chloroplast trnL-F, matK and rbcL support the placement of T. gombea as a distinct species. Tinnea gombea is here assessed as Critically Endangered due to its small population size and restriction to a small area lacking conservation prioritization.

A Quantitative PCR Assay for Detection and Quantification of Fusarium sambucinum

Fusarium sambucinum is an ascomycete that has been isolated from a broad range of plant hosts, including hop (Humulus lupulus L.), where it acts as a causal agent of Fusarium canker, a disease that can impact cone quality and yield in severe cases. Current diagnostic methods rely on isolation of the fungus from plant tissue, a time- and resource-intensive process with limited sensitivity, complicated by the potential presence of other Fusarium spp. that have been reported on hop. Our objective was to develop a rapid and sensitive diagnostic tool to detect and quantify F. sambucinum in plant tissues. Using a modified random amplified polymorphic DNA PCR assay, we identified a F. sambucinum-specific marker that serves as the target in a TaqMan (hydrolysis) probe quantitative PCR (qPCR) assay that can be used to detect F. sambucinum DNA in a background of plant DNA. When used to screen 52 isolates of F. sambucinum and isolates representing 13 other Fusarium spp., the assay was robust in detecting F. sambucinum while discriminating between F. sambucinum and closely related Fusarium spp., including F. venenatum. Furthermore, this assay reliably detects as little as 1 pg of F. sambucinum DNA in a background of total DNA from plant tissue. Within-sample comparisons of this qPCR assay with traditional cultural isolation methods demonstrated the greater sensitivity of the qPCR-based method for detection of F. sambucinum. When used to screen 220 asymptomatic stem samples, the qPCR assay detected F. sambucinum in 100 samples (45.5%); by comparison, F. sambucinum was detected in only 3 samples (1.4%) by culturing methods. Moreover, quantification of F. sambucinum DNA was possible for 60 of these samples, indicating the utility of the qPCR assay for early detection. This assay should be useful in diagnostic and epidemiological applications to detect and quantify F. sambucinum from multiple hosts and environmental samples.

A Detection Assay to Identify Alternative Food Sources of the Two-Spotted Stink Bug, Bathycoelia distincta (Hemiptera: Pentatomidae)

The two-spotted stink bug, Bathycoelia distincta Distant (Hemiptera: Pentatomidae), is a serious pest in South African macadamia orchards. This pest is predominantly controlled using insecticides, thus alternative control methods are essential. The stink bugs arrive as adults in the orchards, during the early nut set season, but little is known about their alternative plant hosts before their arrival. The aim of this study was to develop a PCR-based metabarcoding assay to identify plant material in the gut of B. distincta. Thereafter, the persistence of plant DNA in the gut, after switching food sources, was determined by rearing the stink bugs on Zea mays L. (Cyperales: Poaceae), transferring them to Macadamia sp. and then collecting insects at different time points. As a proof of concept, the assay was tested on insects collected from commercial macadamia orchards to determine if it can identify alternative food sources. The chloroplast gene markers, trnL and trnF, were most successful for plant DNA amplification. The time trial suggested that plant material can be detected 24 h after switching to the alternate food source and one of the samples still contained Z. mays DNA after five days. Various plant species were detected from the orchard collected samples, including known food sources of other stink bugs, such as tea plants (Camellia sinensis L. (Ericales:Theaceae)) and sunflowers (Helianthus annuus L. (Asterales: Asteraceae)). This study provides the first indication of potential alternative food sources of B. distincta. The assay developed in this study can now be implemented for large-scale field surveys to contribute to future integrated pest management strategies.

A premature stop codon in BrFLC2 transcript results in early flowering in oilseed-type Brassica rapa plants

Nonsense-mediated mRNA decay (NMD)-mediated degradation of BrFLC2 transcripts is the main cause of rapid flowering of oilseed-type B. rapa 'LP08' plants. Many Brassica species require vernalization (long-term winter-like cooling) for transition to the reproductive stage. In the past several decades, scientific efforts have been made to discern the molecular mechanisms underlying vernalization in many species. Thus, to identify the key regulators required for vernalization in Brassica rapa L., we constructed a linkage map composed of 7833 single nucleotide polymorphism markers using the late-flowering Chinese cabbage (B. rapa L. ssp. pekinensis) inbred line 'Chiifu' and the early-flowering yellow sarson (B. rapa L. ssp. trilocularis) line 'LP08' and identified a single major QTL on the upper-arm of the chromosome A02. In addition, we compared the transcriptomes of the lines 'Chiifu' and 'LP08' at five vernalization time points, including both non-vernalized and post-vernalization conditions. We observed that BrFLC2 was significantly downregulated in the early flowering 'LP08' and had two deletion sites (one at 4th exon and the other at 3' downstream region) around the BrFLC2 genomic region compared with the BrFLC2 genomic region in 'Chiifu'. Large deletion at 3' downstream region did not significantly affect transcription of both sense BrFLC2 transcript and antisense transcript, BrFLC2as along vernalization time course. However, the other deletion at 4th exon of BrFLC2 resulted in the generation of premature stop codon in BrFLC2 transcript in LP08 line. Cycloheximide treatment of LP08 line showed the de-repressed level of BrFLC2 in LP08, suggesting that low transcript level of BrFLC2 in LP08 might be caused by nonsense-mediated mRNA decay removing the nonsense transcript of BrFLC2. Collectively, this study provides a better understanding of the molecular mechanisms underlying floral transition in B. rapa.

Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2

RNA-dependent RNA polymerases play essential roles in RNA-mediated gene silencing in eukaryotes. In Arabidopsis, RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) physically interacts with DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and their activities are tightly coupled, with Pol IV transcriptional arrest, induced by the nontemplate DNA strand, somehow enabling RDR2 to engage Pol IV transcripts and generate double-stranded RNAs. The double-stranded RNAs are then released from the Pol IV-RDR2 complex and diced into short-interfering RNAs that guide RNA-directed DNA methylation and silencing. Here we report the structure of full-length RDR2, at an overall resolution of 3.1 Å, determined by cryoelectron microscopy. The N-terminal region contains an RNA-recognition motif adjacent to a positively charged channel that leads to a catalytic center with striking structural homology to the catalytic centers of multisubunit DNA-dependent RNA polymerases. We show that RDR2 initiates 1 to 2 nt internal to the 3' ends of its templates and can transcribe the RNA of an RNA/DNA hybrid, provided that 9 or more nucleotides are unpaired at the RNA's 3' end. Using a nucleic acid configuration that mimics the arrangement of RNA and DNA strands upon Pol IV transcriptional arrest, we show that displacement of the RNA 3' end occurs as the DNA template and nontemplate strands reanneal, enabling RDR2 transcription. These results suggest a model in which Pol IV arrest and backtracking displaces the RNA 3' end as the DNA strands reanneal, allowing RDR2 to engage the RNA and synthesize the complementary strand.

Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor

Plants use intracellular nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving the structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. Here, we report the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C Structure-based mutations that disrupt AvrRps4C-RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA-binding domain of AtWRKY41, with similar binding affinities and how effector binding interferes with WRKY-W-box DNA interactions. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity.

A cotransformation system of the unicellular red alga Cyanidioschyzon merolae with blasticidin S deaminase and chloramphenicol acetyltransferase selectable markers

BACKGROUND

The unicellular red alga Cyanidioschyzon merolae exhibits a very simple cellular and genomic architecture. In addition, procedures for genetic modifications, such as gene targeting by homologous recombination and inducible/repressible gene expression, have been developed. However, only two markers for selecting transformants, uracil synthase (URA) and chloramphenicol acetyltransferase (CAT), are available in this alga. Therefore, manipulation of two or more different chromosomal loci in the same strain in C. merolae is limited.

RESULTS

This study developed a nuclear targeting and transformant selection system using an antibiotics blasticidin S (BS) and the BS deaminase (BSD) selectable marker by homologous recombination in C. merolae. In addition, this study has succeeded in simultaneously modifying two different chromosomal loci by a single-step cotransformation based on the combination of BSD and CAT selectable markers. A C. merolae strain that expresses mitochondrion-targeted mSCARLET (with the BSD marker) and mVENUS (with the CAT marker) from different chromosomal loci was generated with this procedure.

CONCLUSIONS

The newly developed BSD selectable marker enables an additional genetic modification to the already generated C. merolae transformants based on the URA or CAT system. Furthermore, the cotransformation system facilitates multiple genetic modifications. These methods and the simple nature of the C. merolae cellular and genomic architecture will facilitate studies on several phenomena common to photosynthetic eukaryotes.

Construction of yeast one-hybrid library and screening of transcription factors regulating LhMYBSPLATTER expression in Asiatic hybrid lilies (Lilium spp.)

BACKGROUND

Anthocyanins, which belong to flavonoids, are widely colored among red-purple pigments in the Asiatic hybrid lilies (Lilium spp.). Transcription factor (TF) LhMYBSPLATTER (formerly known as LhMYB12-Lat), identified as the major kernel protein, regulating the anthocyanin biosynthesis pathway in 'Tiny Padhye' of Tango Series cultivars, which the pigmentation density is high in the lower half of tepals and this patterning is of exceptional ornamental value. However, the research on mechanism of regulating the spatial and temporal expression differences of LhMYBSPLATTER, which belongs to the R2R3-MYB subfamily, is still not well established. To explore the molecular mechanism of directly related regulatory proteins of LhMYBSPLATTER in the anthocyanin pigmentation, the yeast one-hybrid (Y1H) cDNA library was constructed and characterized.

RESULTS

In this study, we describe a yeast one-hybrid library to screen transcription factors that regulate LhMYBSPLATTER gene expression in Lilium, with the library recombinant efficiency of over 98%. The lengths of inserted fragments ranged from 400 to 2000 bp, and the library capacity reached 1.6 × 10⁶ CFU of cDNA insert, which is suitable to fulfill subsequent screening. Finally, seven prey proteins, including BTF3, MYB4, IAA6-like, ERF4, ARR1, ERF WIN1-like, and ERF061 were screened by the recombinant bait plasmid and verified by interaction with the LhMYBSPLATTER promoter. Among them, ERFs, AUX/IAA, and BTF3 may participate in the negative regulation of the anthocyanin biosynthesis pathway in Lilium.

CONCLUSION

A yeast one-hybrid library of lily was successfully constructed in the tepals for the first time. Seven candidate TFs of LhMYBSPLATTER were screened, which may provide a theoretical basis for the study of floral pigmentation.

Response of physiological parameters in Dionaea muscipula J. Ellis teratomas transformed with rolB oncogene

BACKGROUND

Plant transformation with rol oncogenes derived from wild strains of Rhizobium rhizogenes is a popular biotechnology tool. Transformation effects depend on the type of rol gene, expression level, and the number of gene copies incorporated into the plant's genomic DNA. Although rol oncogenes are known as inducers of plant secondary metabolism, little is known about the physiological response of plants subjected to transformation.

RESULTS

In this study, the physiological consequences of rolB oncogene incorporation into the DNA of Dionaea muscipula J. Ellis was evaluated at the level of primary and secondary metabolism. Examination of the teratoma (transformed shoots) cultures of two different clones (K and L) showed two different strategies for dealing with the presence of the rolB gene. Clone K showed an increased ratio of free fatty acids to lipids, superoxide dismutase activity, synthesis of the oxidised form of glutathione, and total pool of glutathione and carotenoids, in comparison to non-transformed plants (control). Clone L was characterised by increased accumulation of malondialdehyde, proline, activity of superoxide dismutase and catalase, total pool of glutathione, ratio of reduced form of glutathione to oxidised form, and accumulation of selected phenolic acids. Moreover, clone L had an enhanced ratio of total triglycerides to lipids and accumulated saccharose, fructose, glucose, and tyrosine.

CONCLUSIONS

This study showed that plant transformation with the rolB oncogene derived from R. rhizogenes induces a pleiotropic effect in plant tissue after transformation. Examination of D. muscipula plant in the context of transformation with wild strains of R. rhizogenes can be a new source of knowledge about primary and secondary metabolites in transgenic organisms.

Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

A novel adenylate isopentenyltransferase 5 regulates shoot branching via the ATTTA motif in Camellia sinensis

BACKGROUND

Shoot branching is one of the important agronomic traits affecting yields and quality of tea plant (Camellia sinensis). Cytokinins (CTKs) play critical roles in regulating shoot branching. However, whether and how differently alternative splicing (AS) variant of CTKs-related genes can influence shoot branching of tea plant is still not fully elucidated.

RESULTS

In this study, five AS variants of CTK biosynthetic gene adenylate isopentenyltransferase (CsA-IPT5) with different 3' untranslated region (3' UTR) and 5' UTR from tea plant were cloned and investigated for their regulatory effects. Transient expression assays showed that there were significant negative correlations between CsA-IPT5 protein expression, mRNA expression of CsA-IPT5 AS variants and the number of ATTTA motifs, respectively. Shoot branching processes induced by exogenous 6-BA or pruning were studied, where CsA-IPT5 was demonstrated to regulate protein synthesis of CsA-IPT5, as well as the biosynthesis of trans-zeatin (tZ)- and isopentenyladenine (iP)-CTKs, through transcriptionally changing ratios of its five AS variants in these processes. Furthermore, the 3' UTR AS variant 2 (3AS2) might act as the predominant AS transcript.

CONCLUSIONS

Together, our results indicate that 3AS2 of the CsA-IPT5 gene is potential in regulating shoot branching of tea plant and provides a gene resource for improving the plant-type of woody plants.

Novel Candidate Genes Differentially Expressed in Glyphosate-Treated Horseweed (Conyza canadensis)

The evolution of herbicide-resistant weed species is a serious threat for weed control. Therefore, we need an improved understanding of how gene regulation confers herbicide resistance in order to slow the evolution of resistance. The present study analyzed differentially expressed genes after glyphosate treatment on a glyphosate-resistant Tennessee ecotype (TNR) of horseweed (Conyza canadensis), compared to a susceptible biotype (TNS). A read size of 100.2 M was sequenced on the Illumina platform and subjected to de novo assembly, resulting in 77,072 gene-level contigs, of which 32,493 were uniquely annotated by a BlastX alignment of protein sequence similarity. The most differentially expressed genes were enriched in the gene ontology (GO) term of the transmembrane transport protein. In addition, fifteen upregulated genes were identified in TNR after glyphosate treatment but were not detected in TNS. Ten of these upregulated genes were transmembrane transporter or kinase receptor proteins. Therefore, a combination of changes in gene expression among transmembrane receptor and kinase receptor proteins may be important for endowing non-target-site glyphosate-resistant C. canadensis.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi's genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Genome editing with CRISPR/Cas9 in Pinus radiata (D. Don)

BACKGROUND

To meet increasing demand for forest-based products and protect natural forests from further deforestation requires increased productivity from planted forests. Genetic improvement of conifers by traditional breeding is time consuming due to the long juvenile phase and genome complexity. Genetic modification (GM) offers the opportunity to make transformational changes in shorter time frames but is challenged by current genetically modified organism (GMO) regulations. Genome editing, which can be used to generate site-specific mutations, offers the opportunity to rapidly implement targeted improvements and is globally regulated in a less restrictive way than GM technologies.

RESULTS

We have demonstrated CRISPR/Cas9 genome editing in P. radiata targeting a single-copy cell wall gene GUX1 in somatic embryogenic tissue and produced plantlets from the edited tissue. We generated biallelic INDELs with an efficiency of 15 % using a single gRNA. 12 % of the transgenic embryogenic tissue was edited when two gRNAs were used and deletions of up to 1.3 kb were identified. However, the regenerated plants did not contain large deletions but had single nucleotide insertions at one of the target sites. We assessed the use of CRISPR/Cas9 ribonucleoproteins (RNPs) for their ability to accomplish DNA-free genome editing in P. radiata. We chose a hybrid approach, with RNPs co-delivered with a plasmid-based selectable marker. A two-gRNA strategy was used which produced an editing efficiency of 33 %, and generated INDELs, including large deletions. Using the RNP approach, deletions found in embryogenic tissue were also present in the plantlets. But, all plants produced using the RNP strategy were monoallelic.

CONCLUSIONS

We have demonstrated the generation of biallelic and monoallelic INDELs in the coniferous tree P. radiata with the CRISPR/Cas9 system using plasmid expressed Cas9 gRNA and RNPs respectively. This opens the opportunity to apply genome editing in conifers to rapidly modify key traits of interest.

Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations

BACKGROUND

Restoration through planting is the dominant strategy to conserve mangrove ecosystems. However, many of the plantations fail to survive. Site and seeding selection matters for planting. The process of afforestation, where individuals were planted in a novel environment, is essentially human-controlled transplanting events. Trying to deepen and expand the understanding of the effects of transplanting on plants, we have performed a seven-year-long reciprocal transplant experiment on Kandelia obovata along a latitudinal gradient.

RESULTS

Combined phenotypic analyses and next-generation sequencing, we found phenotypic discrepancies among individuals from different populations in the common garden and genetic differentiation among populations. The central population with abundant genetic diversity and high phenotypic plasticity had a wide plantable range. But its biomass was reduced after being transferred to other latitudes. The suppressed expression of lignin biosynthesis genes revealed by RNA-seq was responsible for the biomass reduction. Moreover, using whole-genome bisulfite sequencing, we observed modification of DNA methylation in MADS-box genes that involved in the regulation of flowering time, which might contribute to the adaptation to new environments.

CONCLUSIONS

Taking advantage of classical ecological experiments as well as multi-omics analyses, our work observed morphology differences and genetic differentiation among different populations of K. obovata, offering scientific advice for the development of restoration strategy with long-term efficacy, also explored phenotypic, transcript, and epigenetic responses of plants to transplanting events between latitudes.

TCM-Blast for traditional Chinese medicine genome alignment with integrated resources

The traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website ( http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php ) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.

Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches

Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.

Stories that can't be told by SNPs; DNA methylation variation in plant populations

Epigenetic variation has been observed in many plant populations. This variation can influence qualitative and quantitative traits. A key question is whether there is novel information in the epigenome that is not captured by SNP-based genetic markers. The answer likely varies depending on the sources and stability of epigenetic variation as well as the type of population being studied. We consider the epigenetic variation in several plant systems and how this relates to potential for hidden information that could increase our understanding of phenotypic variation.

Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.)

The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.

Revisiting regulatory roles of replication protein A in plant DNA metabolism

This review provides insight into the roles of heterotrimeric RPA protein complexes encompassing all aspects of DNA metabolism in plants along with specific function attributed by individual subunits. It highlights research gaps that need further attention. Replication protein A (RPA), a heterotrimeric protein complex partakes in almost every aspect of DNA metabolism in eukaryotes with its principle role being a single-stranded DNA-binding protein, thereby providing stability to single-stranded (ss) DNA. Although most of our knowledge of RPA structure and its role in DNA metabolism is based on studies in yeast and animal system, in recent years, plants have also been reported to have diverse repertoire of RPA complexes (formed by combination of different RPA subunit homologs arose during course of evolution), expected to be involved in plethora of DNA metabolic activities. Here, we have reviewed all studies regarding role of RPA in DNA metabolism in plants. As combination of plant RPA complexes may vary largely depending on number of homologs of each subunit, next step for plant biologists is to develop specific functional methods for detailed analysis of biological roles of these complexes, which we have tried to formulate in our review. Besides, complete absence of any study regarding regulatory role of posttranslational modification of RPA complexes in DNA metabolism in plants, prompts us to postulate a hypothetical model of same in light of information from animal system. With our review, we envisage to stimulate the RPA research in plants to shift its course from descriptive to functional studies, thereby bringing a new angle of studying dynamic DNA metabolism in plants.

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

BACKGROUND

The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species.

RESULTS

Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa.

CONCLUSIONS

This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice

BACKGROUND

Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress.

RESULTS

Our results showed that external N deficiency could decrease seed N content and plant growth of the overexpression line. During the filial growth, we found that the low parent seed nitrogen (LPSN) in the overexpression line could lead to a decrease in the filial seed nitrogen content, total plant nitrogen content, yield, and OsNAR2.1 expression (28, 35, 23, and 55%, respectively) compared with high parent seed nitrogen (HPSN) in high nitrogen external supply. However, such decreases were not observed in wild type. Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type.

CONCLUSIONS

We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1, resulting in a heritable phenotype of N deficiency over two generations of the overexpression line.

Differential DNA methylation and gene expression during development of reproductive and vegetative organs in Ilex species

Differential epigenetic (DNA cytosine methylation) and gene expression patterns were investigated in reproductive and vegetative organs from Ilex paraguariensis and I. dumosa, at distinct developmental stages. We aimed at contributing towards elucidating major molecular changes underlying the sexual differentiation processes which, in these dioecious species, are completely unknown. Simultaneously, as a first step towards the development of an early sexing system, we searched for promising molecular markers. This was assessed through Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism on cDNA (cDNA-AFLP) techniques, applying discriminant multivariate analyses, and bioinformatic characterization of differential fragments. A significant positive correlation was found between epigenetic and indirect 'genetic' information for both species, indicating influence of the genetic background on the epigenetic variation. Higher epigenetic than genetic diversities were estimated. Our outcomes showed up to 1.86 times more representation of mCG subepiloci than mCCG in all organs sampled. Along the maturing stages of floral buds, the frequency of mCG evidenced an incremental trend, whereas mCCG and unmethylated conditions showed opposite tendencies. Reproductive and vegetative samples tended to cluster apart based on epigenetic patterns; at gene expression level, organs exhibited clear-cut distinctive patterns, nonetheless profiles of young leaves and floral primordia resemble. Epigenetic and expression data allowed discrimination of I. dumosa´s samples according to the gender of the donor; more elusive patterns were observed for I. paraguariensis. In total, 102 differentially methylated and expressed fragments were characterized bioinformatically. Forty-three were annotated in various functional categories; four candidate markers were validated through qPCR, finding statistical differences among organs but not among sexes. The methylation condition of epilocus C13m33 appears as indicative of gender in both species. Thirty-three organ-specific and 34 gender-specific methylated markers were discriminated and deserve further research, particularly those expressed in leaves. Our study contributes concrete candidate markers with potential for practical application.

PNA-functionalized magnetic microbeads as substrates for enzyme-labelled voltammetric genoassay for DNA sensing applied to identification of GMO in food

A novel enzyme-labelled voltammetric magnetogenoassay for DNA sensing based on the use of carboxyl-surface coated magnetic microbeads functionalized with PNA probes and subsequent read-out on screen-printed electrode (SPE) substrates was developed. The assay was validated for determination of non-amplified genomic DNA from genetically modified Roundup Ready soy. Outstanding performance with respect to other genoassays requiring preliminary amplification of target DNA via PCR was demonstrated. The analytical performance was also improved compared to previous methods based on the immobilization of the same PNA probes on SPE substrates, since the method was found capable of achieving LOD and LOQ of 415 fM and 995 fM, respectively. The ability of the magnetogenoassay to detect the presence of Roundup Ready soy DNA sequence was tested on genomic DNA extract from European Reference Material soy flours, demonstrating the capability of the method to match the European Union regulation for labelling of food containing a percentage of GM products greater than 0,9%.

Perspective: 50 years of plant chromosome biology

The past 50 years has been the greatest era of plant science discovery, and most of the discoveries have emerged from or been facilitated by our knowledge of plant chromosomes. At last we have descriptive and mechanistic outlines of the information in chromosomes that programs plant life. We had almost no such information 50 years ago when few had isolated DNA from any plant species. The important features of genes have been revealed through whole genome comparative genomics and testing of variants using transgenesis. Progress has been enabled by the development of technologies that had to be invented and then become widely available. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have played extraordinary roles as model species. Unexpected evolutionary dramas were uncovered when learning that chromosomes have to manage constantly the vast numbers of potentially mutagenic families of transposons and other repeated sequences. The chromatin-based transcriptional and epigenetic mechanisms that co-evolved to manage the evolutionary drama as well as gene expression and 3-D nuclear architecture have been elucidated these past 20 years. This perspective traces some of the major developments with which I have become particularly familiar while seeking ways to improve crop plants. I draw some conclusions from this look-back over 50 years during which the scientific community has (i) exposed how chromosomes guard, readout, control, recombine, and transmit information that programs plant species, large and small, weed and crop, and (ii) modified the information in chromosomes for the purposes of genetic, physiological, and developmental analyses and plant improvement.

Essential Oil Composition and DNA Barcode and Identification of Aniba species (Lauraceae) Growing in the Amazon Region

Lauraceae species are widely represented in the Amazon, presenting a significant essential oil yield, large chemical variability, various biological applications, and high economic potential. Its taxonomic classification is difficult due to the accentuated morphological uniformity, even among taxa from a different genus. For this reason, the present work aimed to find chemical and molecular markers to discriminate Aniba species collected in the Pará State (Brazil). The chemical composition of the essential oils from Aniba canelilla, A. parviflora, A. rosaeodora, and A. terminalis were grouped by multivariate statistical analysis. The major compounds were rich in benzenoids and terpenoids such as 1-nitro-2-phenylethane (88.34-70.85%), linalool (15.2-75.3%), α-phellandrene (36.0-51.8%), and β-phellandrene (11.6-25.6%). DNA barcodes were developed using the internal transcribed spacer (ITS) nuclear region, and the matK, psbA-trnH, rbcL, and ycf1 plastid regions. The markers psbA-trnH and ITS showed the best discrimination for the species, and the phylogenic analysis in the three- (rbcL + matK + trnH - psbA and rbcL + matK + ITS) and four-locus (rbcL + matK + trnH - psbA + ITS) combination formed clades with groups strongly supported by the Bayesian inference (BI) (PP:1.00) and maximum likelihood (ML) (BS ≥ 97%). Therefore, based on statistical multivariate and phylogenetic analysis, the results showed a significant correlation between volatile chemical classes and genetic characteristics of Aniba species.

Quantification of Actaea racemosa L. (black cohosh) from some of its potential adulterants using qPCR and dPCR methods

The demand for popular natural health products (NHPs) such as Black Cohosh is increasing considerably, which in turn challenges quality assurance (QA) throughout the supply chain. To detect and quantify the target species present in a given NHP, DNA-based molecular techniques such as Real-time quantitative PCR (qPCR) and digital PCR (dPCR) are standard tools in the food and pathogen testing industries. There is a gap in the literature concerning validated quantitative PCR methods for botanicals that can be utilized for QA and good manufacturing practices. The objective of this study is to develop an efficient quantification method using qPCR and dPCR techniques for the detection and quantification of Actaea racemosa (Black cohosh) NHPs from its potential adulterants. These developed methods are validated for applicability on commercial NHPs. Species-specific hydrolysis probe assays were designed to analyze the black cohosh NHPs using qPCR and dPCR techniques. The results confirmed that the developed qPCR and dPCR methods are highly precise for identifying and quantifying black cohosh NHPs, indicating their potential applicability in future routine industrial and laboratory testing. This enables a single qPCR test to determine not only the presence of a specific botanical, but also the amount when mixed with an adulterant.

A 1232 bp upstream sequence of glutamine synthetase 1b from Eichhornia crassipes is a root-preferential promoter sequence

BACKGROUND

Glutamine synthetase (GS) acts as a key enzyme in plant nitrogen (N) metabolism. It is important to understand the regulation of GS expression in plant. Promoters can initiate the transcription of its downstream gene. Eichhornia crassipes is a most prominent aquatic invasive plant, which has negative effects on environment and economic development. It also can be used in the bioremediation of pollutants present in water and the production of feeding and energy fuel. So identification and characterization of GS promoter in E. crassipes can help to elucidate its regulation mechanism of GS expression and further to control its N metabolism.

RESULTS

A 1232 bp genomic fragment upstream of EcGS1b sequence from E. crassipes (EcGS1b-P) has been cloned, analyzed and functionally characterized. TSSP-TCM software and PlantCARE analysis showed a TATA-box core element, a CAAT-box, root specific expression element, light regulation elements including chs-CMA1a, Box I, and Sp1 and other cis-acting elements in the sequence. Three 5'-deletion fragments of EcGS1b upstream sequence with 400 bp, 600 bp and 900 bp length and the 1232 bp fragment were used to drive the expression of β-glucuronidase (GUS) in tobacco. The quantitative test revealed that GUS activity decreased with the decreasing of the promoter length, which indicated that there were no negative regulated elements in the EcGS1-P. The GUS expressions of EcGS1b-P in roots were significantly higher than those in leaves and stems, indicating EcGS1b-P to be a root-preferential promoter. Real-time Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) analysis of EcGS1b gene also showed higher expression in the roots of E.crassipes than in stems and leaves.

CONCLUSIONS

EcGS1b-P is a root-preferential promoter sequence. It can specifically drive the transcription of its downstream gene in root. This study will help to elucidate the regulatory mechanisms of EcGS1b tissue-specific expression and further study its other regulatory mechanisms in order to utilize E.crassipes in remediation of eutrophic water and control its overgrowth from the point of nutrient metabolism.

Microsatellite-based association mapping for agronomic traits in mungbean (Vigna radiata L. Wilczek)

Mungbean (Vigna radiata L. Wilczek) is one of the most important warm season food legumes which contributes significantly towards nutritional security and environmental sustainability. Marker-trait association (MTA) for agronomic characters offer opportunities to deploy marker-assisted breeding for genetic amelioration of crops. This investigation was carried out with an objective to decipher population genetic structure of diverse Vigna accessions and detect microsatellite loci linked to major agronomic traits for mungbean improvement. The study was initiated with 290 diverse Vigna accessions including wild and cultivated accessions. A mungbean yellow mosaic India virus (MYMIV)-resistant association mapping panel was constructed to minimize the effect of yellow mosaic disease on crop performance. Among these, 117 accessions including 55 cultivated and 63 wild accessions were found highly resistant to MYMIV. After multi-environment phenotyping, a panel of 70 MYMIV-resistant mungbean accessions was subjected to analysis for assessing the population genetic structure as well as MTA for important agronomic traits. There was sufficient genetic variation among the 70-mungbean genotypes as depicted by 91 microsatellite markers. Population genetic structure analysis grouped the genotypes into five subpopulations. The locus GMES0162 (LG4) was strongly associated with days to first flowering, whereas loci CEDG 035 (LG8), DMB SSR001 (LG6), DMB SSR008 (LG4) and CEDG 168 (LG11) were associated with pod number. These marker-trait associations will be helpful in genetic improvement of mungbean through molecular breeding.

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.

Plant DNA Barcoding Principles and Limits: A Case Study in the Genus Vanilla

Powerful DNA barcodes have been much more difficult to define in plants than in animals. In 2009, the international Consortium for the Barcoding Of Life (CBOL) chose the combination of the chloroplast genes (rbcL + matK) as the proposed official barcode for plants. However, this system has got important limits. First, any barcode system will only be useful if there is a clear barcode gap and if species are monophyletic. Second, chloroplast and mitochondrial (COI gene used for animals) barcodes will not be usable for discriminating hybrid species. Moreover, it was also shown that, using chloroplast regions, maximum species discrimination would be around 70% and very variable among plant groups. This is why many authors have more recently advocated for the addition of the nuclear ITS region to this barcode because it reveals more variations and allows the resolution of hybrid or closely related species. We tested different chloroplast genes (rbcL, matK, psaB, psbC) and the nuclear ITS region in the genus Vanilla, a taxonomically complex group and therefore a good model to test for the efficiency of different barcode systems. We found that the CBOL official barcode system performed relatively poorly in Vanilla (76% species discrimination), and we demonstrate that adding ITS to this barcode system allows to increase resolution (for closely related species and to the subspecies level) and to identify hybrid species. The best species discrimination attained was 96.2% because of one paraphyletic species that could not be resolved.

MfbHLH38, a Myrothamnus flabellifolia bHLH transcription factor, confers tolerance to drought and salinity stresses in Arabidopsis

BACKGROUND

The basic helix-loop-helix (bHLH) proteins, a large transcription factors family, are involved in plant growth and development, and defensive response to various environmental stresses. The resurrection plant Myrothamnus flabellifolia is known for its extremely strong drought tolerance, but few bHLHs taking part in abiotic stress response have been unveiled in M. flabellifolia.

RESULTS

In the present research, we cloned and characterized a dehydration-inducible gene, MfbHLH38, from M. flabellifolia. The MfbHLH38 protein is localized in the nucleus, where it may act as a transcription factor. Heterologous expression of MfbHLH38 in Arabidopsis improved the tolerance to drought and salinity stresses, as determined by the studies on physiological indexes, such as contents of chlorophyll, malondialdehyde (MDA), proline (Pro), soluble protein, and soluble sugar, water loss rate of detached leaves, reactive oxygen species (ROS) accumulation, as well as antioxidant enzyme activities. Besides, MfbHLH38 overexpression increased the sensitivity of stomatal closure to mannitol and abscisic acid (ABA), improved ABA level under drought stress, and elevated the expression of genes associated with ABA biosynthesis and ABA responding, sucha as NCED3, P5CS, and RD29A.

CONCLUSIONS

Our results presented evidence that MfbHLH38 enhanced tolerance to drought and salinity stresses in Arabidopsis through increasing water retention ability, regulating osmotic balance, decreasing stress-induced oxidation damage, and possibly participated in ABA-dependent stress-responding pathway.

Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

BACKGROUND

The Lycoris genus includes many ornamentally and medicinally important species. Polyploidization and hybridization are considered modes of speciation in this genus, implying great genetic diversity. However, the lack of effective molecular markers has limited the genetic analysis of this genus.

RESULTS

In this study, mining of EST-SSR markers was performed using transcriptome sequences of L. aurea, and 839 primer pairs for non-redundant EST-SSRs were successfully designed. A subset of 60 pairs was randomly selected for validation, of which 44 pairs could amplify products of the expected size. Cross-species transferability of the 60 primer pairs among Lycoris species were assessed in L. radiata Hreb, L. sprengeri Comes ex Baker, L. chinensis Traub and L. anhuiensis, of which between 38 to 77% of the primers were able to amplify products in these Lycoris species. Furthermore, 20 and 10 amplification products were selected for sequencing verification in L. aurea and L. radiata respectively. All products were validated as expected SSRs. In addition, 15 SSRs, including 10 sequence-verified and 5 unverified SSRs were selected and used to evaluate the genetic diversity of seven L. radiata lines. Among these, there were three sterile lines, three fertile lines and one line represented by the offspring of one fertile line. Unweighted pair group method with arithmetic mean analysis (UPGMA) demonstrated that the outgroup, L. aurea was separated from L. radiata lines and that the seven L. radiata lines were clustered into two groups, consistent with their fertility. Interestingly, even a dendrogram with 34 individuals representing the seven L. radiata lines was almost consistent with fertility.

CONCLUSIONS

This study supplies a pool of potential 839 non-redundant SSR markers for genetic analysis of Lycoris genus, that present high amplification rate, transferability and efficiency, which will facilitate genetic analysis and breeding program in Lycoris.

Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines

BACKGROUND

Flax (Linum usitatissimum L.) is grown for fiber and seed in many countries. Flax cultivars differ in the oil composition and, depending on the ratio of fatty acids, are used in pharmaceutical, food, or paint industries. It is known that genes of SAD (stearoyl-ACP desaturase) and FAD (fatty acid desaturase) families play a key role in the synthesis of fatty acids, and some alleles of these genes are associated with a certain composition of flax oil. However, data on genetic polymorphism of these genes are still insufficient.

RESULTS

On the basis of the collection of the Institute for Flax (Torzhok, Russia), we formed a representative set of 84 cultivars and lines reflecting the diversity of fatty acid composition of flax oil. An approach for the determination of full-length sequences of SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes using the Illumina platform was developed and deep sequencing of the 6 genes in 84 flax samples was performed on MiSeq. The obtained high coverage (about 400x on average) enabled accurate assessment of polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes and evaluation of cultivar/line heterogeneity. The highest level of genetic diversity was observed for FAD3A and FAD3B genes - 91 and 62 polymorphisms respectively. Correlation analysis revealed associations between particular variants in SAD and FAD genes and predominantly those fatty acids whose conversion they catalyze: SAD - stearic and oleic acids, FAD2 - oleic and linoleic acids, FAD3 - linoleic and linolenic acids. All except one low-linolenic flax cultivars/lines contained both the substitution of tryptophan to stop codon in the FAD3A gene and histidine to tyrosine substitution in the FAD3B gene, while samples with only one of these polymorphisms had medium content of linolenic acid and cultivars/lines without them were high-linolenic.

CONCLUSIONS

Genetic polymorphism of SAD and FAD genes was evaluated in the collection of flax cultivars and lines with diverse oil composition, and associations between particular polymorphisms and the ratio of fatty acids were revealed. The achieved results are the basis for the development of marker-assisted selection and DNA-based certification of flax cultivars.

Chromosome-Level Reference Genome and Population Genomic Analysis Provide Insights into the Evolution and Improvement of Domesticated Mulberry (Morus alba)

Mulberry (Morus spp.) is the sole plant consumed by the domesticated silkworm. However, the genome of domesticated mulberry has not yet been sequenced, and the ploidy level of this species remains unclear. Here, we report a high-quality, chromosome-level domesticated mulberry (Morus alba) genome. Analysis of genomic data and karyotype analyses confirmed that M. alba is a diploid with 28 chromosomes (2n = 2x = 28). Population genomic analysis based on resequencing of 134 mulberry accessions classified domesticated mulberry into three geographical groups, namely, Taihu Basin of southeastern China (Hu mulberry), northern and southwestern China, and Japan. Hu mulberry had the lowest nucleotide diversity among these accessions and demonstrated obvious signatures of selection associated with environmental adaptation. Further phylogenetic analysis supports a previous proposal that multiple domesticated mulberry accessions previously classified as different species actually belong to one species. This study expands our understanding of genome evolution of the genus Morus and population structure of domesticated mulberry, which would facilitate mulberry breeding and improvement.

A point mutation in the photosystem I P700 chlorophyll a apoprotein A1 gene confers variegation in Helianthus annuus L

Even a point mutation in the psaA gene mediates chlorophyll deficiency. The role of the plastid signal may perform the redox state of the compounds on the acceptor-side of PSI. Two extranuclear variegated mutants of sunflower, Var1 and Var33, were investigated. The yellow sectors of both mutants were characterized by an extremely low chlorophyll and carotenoid content, as well as poorly developed, unstacked thylakoid membranes. A full-genome sequencing of the cpDNA revealed mutations in the psaA gene in both Var1 and Var33. The cpDNA from the yellow sectors of Var1 differs from those in the wild type by only a single, non-synonymous substitution (Gly734Glu) in the psaA gene, which encodes a subunit of photosystem (PS) I. In the cpDNA from the yellow sectors of Var33, the single-nucleotide insertion in the psaA gene was revealed, leading to frameshift at the 580 amino acid position. Analysis of the photosynthetic electron transport demonstrated an inhibition of the PSI and PSII activities in the yellow tissues of the mutant plants. It has been suggested that mutations in the psaA gene of both Var1 and Var33 led to the disruption of PSI. Due to the non-functional PSI, photosynthetic electron transport is blocked, which, in turn, leads to photodamage of PSII. These data are confirmed by immunoblotting analysis, which showed a significant reduction in PsbA in the yellow leaf sectors, but not PsaA. The expression of chloroplast and nuclear genes encoding the PSI subunits (psaA, psaB, and PSAN), the PSII subunits (psbA, psbB, and PSBW), the antenna proteins (LHCA1, LHCB1, and LHCB4), the ribulose 1.5-bisphosphate carboxylase subunits (rbcL and RbcS), and enzymes of chlorophyll biosynthesis were down-regulated in the yellow leaf tissue. The extremely reduced transcriptional activity of the two protochlorophyllide oxidoreductase (POR) genes involved in chlorophyll biosynthesis is noteworthy. The disruption of NADPH synthesis, due to the non-functional PSI, probably led to a significant reduction in NADPH-protochlorophyllide oxidoreductase in the yellow sectors of Var1 and Var33. A dramatic decrease in chlorophyllide was shown in the yellow sectors. A reduction in NADPH-protochlorophyllide oxidoreductase, along with photodegradation, has been suggested as a result of chlorophyll deficiency.

The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri

Gene copy number variation is a predominant mechanism used by organisms to respond to selective pressures from the environment. This often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity in Amaranthus palmeri: a massive, ∼400-kb extrachromosomal circular DNA (eccDNA) that harbors the 5-ENOYLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) gene and 58 other genes whose encoded functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of these 59 genes, with high expression of EPSPS, as well as genes coding for aminotransferases, zinc finger proteins, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is composed of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and waterhemp (Amaranthus tuberculatus) suggests that higher order chromatin interactions contribute to the genomic origins of the A. palmeri eccDNA replicon structure.