Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation

Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships

BACKGROUND

The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely.

METHODS AND RESULTS

We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis.

CONCLUSION

The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.

Genome-wide analysis of cellulose synthase gene superfamily in Tectona grandis L.f

This study aimed to explore Cellulose synthase gene superfamily of teak, and its evolutionary relationship with homologous genes of other woody species. The incidence of evolutionary events like gene duplication and gene loss, influence of the selection pressure, and consequent adaptive functional divergence of the duplicated TgCes gene were assessed alongside it's role in wood coloration. This study identified 39 full-length non-redundant proteins belonging to CesA and Csl gene families. TgCesA and TgCsl proteins with Cellulose synthase domain repeats indicated tandem gene duplication and probable genetic variability, enabling local adaptation. Further, multi-domain protein (MYB-like DNA-binding domain and CesA domain) with maximum introns was also identified indicating gene fusion and formation of complex protein with novel functions. Phylogenetic analysis grouped the genes into seven subfamilies (CesA, CslA, CslC, CslD, CslE, CslG, and CslM) with each undergoing gene duplication and loss along their evolutionary history. Post-species gene duplications and probable neofunctionalization were identified in TgCesA and TgCsl gene families. Each subfamily was found to be under strong purifying selection with a few or no sites under positive selection. Functional divergence analysis further revealed site-specific selective constraints in CesA and Csl genes of the teak Cellulose synthase gene family. Furthermore, protein-protein interaction network analysis identified co-expression of Cellulose synthase gene with flavonoid 3',5'-hydroxylase (F3'5'H, CYP75A), involved in the biosynthesis of xylem anthocyanin compounds, probably responsible for wood coloration. This study thus offers a foundation for future research in wood formation and wood property traits specific to teak and its provenances.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03927-6.

Structure, Synthesis, and Bioassays of Sex Pheromone for Pyrausta machaeralis (Lepidoptera: Crambidae)

The leaf skeletonizer, Pyrausta machaeralis (Lepidoptera: Crambidae), is a serious insect pest of teak (Tectona grandis) in China. The application of insect pheromones is widely applied as an environmentally friendly technology for integrated pest management (IPM). In the present study, crude extracts of sex pheromone glands of calling P. machaeralis females were collected and then analyzed using gas chromatography/electroantennographic detection (GC/EAD) and gas chromatography-mass spectrometry (GC-MS). The combination of infrared spectroscopy (IR) and nuclear magnetic resonance (NMR) spectrometry was used for structure identification. Afterward, their electrophysiological and behavioral activity was evaluated in the laboratory and field. Herein, we eventually determined two active components, E-11-tetradecenyl acetate (E11-14:Ac) and Z-11-tetradecenyl acetate (Z11-14:Ac), at a ratio of 96:4, as the sex pheromone of P. machaeralis. The identification of sex pheromones would facilitate the development of efficient strategies for monitoring and controlling the field populations of P. machaeralis.

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its first sources of diversity and little is known about the genetic origin and genetic variability. Thus, this study aimed to investigate the genetic diversity and genetic population structure existing in a representative teak germplasm bank collection. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 3 giga bases per sample, the sequences are aligned using the genome, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four populations with considerable genetic variability between and within them. While the genetic variability in teak is generally known to be narrow, this study confirmed the presence of genetic variability scale in teak, which is contrary to what was initially expected.

Genomic and Transcriptional Profiling Analysis and Insights into Rhodomyrtone Yield in Rhodomyrtus tomentosa (Aiton) Hassk

Rhodomyrtus tomentosa is a source of a novel antibiotic, rhodomyrtone. Because of the increasing industrial demand for this compound, germplasm with a high rhodomyrtone content is the key to sustainable future cultivation. In this study, rhodomyrtone genotypes were verified using the plastid genomic region marker matK and nuclear ribosomal internal transcribed spacer ITS. These two DNA barcodes proved to be useful tools for identifying different rhodomyrtone contents via the SNP haplotypes C569T and A561G, respectively. The results were correlated with rhodomyrtone content determined via HPLC. Subsequently, R. tomentosa samples with high- and low-rhodomyrtone genotypes were collected for de novo transcriptome and gene expression analyses. A total of 83,402 unigenes were classified into 25 KOG classifications, and 74,102 annotated unigenes were obtained. Analysis of differential gene expression between samples or groups using DESeq2 revealed highly expressed levels related to rhodomyrtone content in two genotypes. semiquantitative RT-PCR further revealed that the high rhodomyrtone content in these two genotypes correlated with expression of zinc transporter protein (RtZnT). In addition, we found that expression of RtZnT resulted in increased sensitivity of R. tomentosa under ZnSO4 stress. The findings provide useful information for selection of cultivation sites to achieve high rhodomyrtone yields in R. tomentosa.

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.

The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding

The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.

Amplification, sequencing and characterization of pectin methyl esterase inhibitor 51 gene in Tectona grandis L.f

Tectona grandis L.f. (Teak), a very important source of incomparable timber, withstands a wide range of tropical deciduous conditions. We achieved partial amplification of pectin methylesterase inhibitor 51 (PMEI) gene in teak by E. pilularis cinnamoyl Co-A reductase (CCR) gene specific primer. The amplified teak gene was of 750 bp, 79% identity and 97% query cover with PMEI of Sesamum indicum. The phylogenetic tree clustered the amplified gene with PMEI of database plant species, Erythranthe guttata and Sesamum indicum (87% bootstrap value). On conversion to amino acid sequence, the obtained protein comprised 237 amino acids. However, PMEI region spanned from 24 to 171 amino acids, 15.94 kDa molecular weight, 8.97 pI value and C₆₉₇H₁₁₁₇N₁₉₉O₂₁₁S₉ molecular formula with four conserved cysteine residues as disulfide bridges. 25.9 % protein residues were hydrophilic, 42.7% hydrophobic and 31.2% neutral. Teak 3D PMEI protein structure corresponded well with Arabidopsis thaliana and Actinidia deliciosa PMEIs. The gene maintains integrity of pectin component of middle lamella of primary cell wall and confers tolerance against various kinds of stresses. Teak conferred with overexpression of PMEI may secure a wide adaptability as well as luxuriant timber productivity and quality in adverse/ fluctuating/ scarce climatic and environmental conditions of tropical forests.

Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp

Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

BACKGROUND

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees.

RESULTS

For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR.

CONCLUSIONS

We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular biology have revolutionized traditional plant breeding based on visual phenotype assessment: the development of different types of molecular markers has made genotype selection possible. Marker-assisted breeding can significantly accelerate the breeding process, but this method has not been shown to be effective for selection of complex traits on forest trees. This new method of genomic selection is based on the analysis of all effects of quantitative trait loci (QTLs) using a large number of molecular markers distributed throughout the genome, which makes it possible to assess the genomic estimated breeding value (GEBV) of an individual. This approach is expected to be much more efficient for forest tree improvement than traditional breeding. Here, we review the current state of the art in the application of genomic selection in forest tree breeding and discuss different methods of genotyping and phenotyping. We also compare the accuracies of genomic prediction models and highlight the importance of a prior cost-benefit analysis before implementing genomic selection. Perspectives for the further development of this approach in forest breeding are also discussed: expanding the range of species and the list of valuable traits, the application of high-throughput phenotyping methods, and the possibility of using epigenetic variance to improve of forest trees.

Oxford Nanopore sequencing: new opportunities for plant genomics?

DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

BACKGROUND

The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.

FINDINGS

Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.

CONCLUSION

Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

BACKGROUND

The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes.

FINDINGS

Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars.

CONCLUSION

Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.

Pharmaceutical resource discovery from traditional medicinal plants: Pharmacophylogeny and pharmacophylogenomics

The worldwide botanical and medicinal culture diversity are astonishing and constitute a Pierian spring for innovative drug R&D. Here, the latest awareness and the perspectives of pharmacophylogeny and pharmacophylogenomics, as well as their expanding utility in botanical drug R&D, are systematically summarized and highlighted. Chemotaxonomy is based on the fact that closely related plants contain the same or similar chemical profiles. Correspondingly, it is better to combine morphological characters, DNA markers and chemical markers in the inference of medicinal plant phylogeny. Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic effects, thus forming the core of pharmacophylogeny. Here we systematically review and comment on the versatile applications of pharmacophylogeny in (1) looking for domestic resources of imported drugs, (2) expanding medicinal plant resources, (3) quality control, identification and expansion of herbal medicines, (4) predicting the chemical constituents or active ingredients of herbal medicine and assisting in the identification and determination of chemical constituents, (5) the search for new drugs sorting out, and (6) summarizing and improving herbal medicine experiences, etc. Such studies should be enhanced within the context of deeper investigations of molecular biology and genomics of traditional medicinal plants, phytometabolites and metabolomics, and ethnomedicine-based pharmacological activity, thus enabling the sustainable conservation and utilization of traditional medicinal resources.

Cross-amplification of microsatellite markers across agarwood-producing species of the Aquilarieae tribe (Thymelaeaceae)

Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A. crassna, A. malaccensis, and A. sinensis), on ten other agarwood-producing species, including members of Aquilaria (A. beccariana, A. hirta, A. microcarpa, A. rostrata, A. rugosa, A. subintegra, and A. yunnanensis) and Gyrinops (G. caudata, G. versteegii, and G. walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.

De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections

Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.

Ecotypes or phenotypic plasticity-The aquatic and terrestrial forms of Helosciadium repens (Apiaceae)

Morphological and ecological differences of two forms of Helosciadium repens are known and described in the literature: aquatic and terrestrial. However, their taxonomic status is currently unknown. The question whether they are genotypically adapted to specific environmental conditions or are those differences a result of phenotypic plasticity is addressed in this study.SSR and ISSR data were used to uncover genotypic differences. Data from drought stress experiments (system water content and relative water content of leaves) were used to evaluate the response to water as an environmental factor. The stomatal index of both forms grown under different water treatments was analyzed.The principal component analysis of the ISSR data revealed no clustering that would correspond with ecotypes. The diversity parameters of the SSR data showed no significant differences. The aquatic populations showed a tendency toward heterozygosity, while the terrestrial ones showed a bias toward homozygosity. Both forms responded similarly to the changes in water availability, with newly produced leaves after drought stress that were better adapted to repeated drought stress. Stomatal indices were higher in plants from aquatic habitats, but these differences disappeared when the plants were grown in soil.The observed responses indicate that the differences between forms are due to phenotypic plasticity.

Physiological and molecular responses to drought stress in teak (Tectona grandis L.f.)

Drought stress is an increasingly common and worrying phenomenon because it causes a loss of production in both agriculture and forestry. Teak is a tropical tree which needs alternating rainy and dry seasons to produce high-quality wood. However, a robust understanding about the physiological characteristics and genes related to drought stress in this species is lacking. Consequently, after applying moderate and severe drought stress to teak seedlings, an infrared gas analyzer (IRGA) was used to measure different parameters in the leaves. Additionally, using the root transcriptome allowed finding and analyzing the expression of several drought-related genes. As a result, in both water deficit treatments a reduction in photosynthesis, transpiration, stomatal conductance and leaf relative water content was found. As well, an increase in free proline levels and intrinsic water use efficiency was found when compared to the control treatment. Furthermore, 977 transcripts from the root contigs showed functional annotation related to drought stress, and of these, TgTPS1, TgDREB1, TgAREB1 and TgPIP1 were selected. The expression analysis of those genes along with TgHSP1, TgHSP2, TgHSP3 and TgBI (other stress-related genes) showed that with moderate treatment, TgTPS1, TgDREB1, TgAREB1, TgPIP1, TgHSP3 and TgBI genes had higher expression than the control treatment, but with severe treatment only TgTPS1 and TgDREB1 showed higher expression than the control treatment. At the end, a schematic model for the physiological and molecular strategies under drought stress in teak from this study is provided. In conclusion, these physiological and biochemical adjustments in leaves and genetic changes in roots under severe and prolonged water shortage situations can be a limiting factor for teak plantlets' growth. Further studies of those genes under different biotic and abiotic stress treatments are needed.

A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

Background

Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits.

Findings

To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage Pacific Biosciences long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes, which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs.

Conclusions

In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.

Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.)

Despite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read sequencing (LRS) systems, including the Oxford Nanopore Technologies (ONT) minION, have become popular options for de novo genome assembly and structural variant characterisation. The current high error rate often requires substantial post-sequencing correction and would appear to prevent the adoption of this system for SNP genotyping, but nanopore sequencing errors are largely random. Using low coverage ONT minION sequencing for genotyping of pre-validated SNP loci was examined in 9 canola doubled haploids. The minION genotypes were compared to the Illumina sequences to determine the extent and nature of genotype discrepancies between the two systems. The significant increase in read length improved alignment to the genome and the absence of classical SRS biases results in a more even representation of the genome. Sequencing errors are present, primarily in the form of heterozygous genotypes, which can be removed in completely homozygous backgrounds but requires more advanced bioinformatics in heterozygous genomes. Developments in this technology are promising for routine genotyping in the future.

Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties

Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.