Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

Abstract Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

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Pseudopestalotiopsis gilvanii sp. nov. and Neopestalotiopsis formicarum leaves spot pathogens from guarana plant: a new threat to global tropical hosts

Phytotaxa ◽

10.11646/phytotaxa.489.2.2 ◽

2021 ◽

Vol 489 (2) ◽

pp. 121-139

Author(s):

GILVANA F. GUALBERTO ◽

ARICLÉIA DE M. CATARINO ◽

THIAGO F. SOUSA ◽

JEFERSON C. CRUZ ◽

ROGÉRIO E. HANADA ◽

...

Keyword(s):

Plant Pathogen ◽

Elaeis Guineensis ◽

Elongation Factor ◽

Leaf Tissue ◽

Euterpe Oleracea ◽

Internal Transcribed Spacer Region ◽

Tropical Regions ◽

Tropical Plants ◽

Wide Range ◽

Genes Encoding

Pestalotioid species (Pestalotiopsis, Pseudopestalotiopsis and Neopestalotiopsis) cause extremely damaging diseases in a wide range of hosts across the word. Recently, pestalotioid strains isolated from damaged guarana leaf tissue were subject to morphological and molecular characterization. Six monosporic isolates were obtained and analysed based on the following conidial characters: length, width, septation, absence or presence of basal appendage, number and length of apical appendages. For phylogenetic inference, sequences of the Internal Transcribed Spacer region (ITS), partial sequences of the genes encoding the translation elongation factor 1-α (tef1-α) and β-tubulin (tub2) were used. Three out of six strains analysed were identified as Neopestalotiopsis formicarum, while the three other isolates are described here as a new species of Pseudopestalotiopsis, named Ps. gilvanii sp. nov.. The pathogenicity of N. formicarum and Ps. gilvanii were confirmed following Koch’s postulate. Besides guarana, the potential of N. formicaram and Ps. gilvanii to cause diseases in other economically important tropical plants were investigated. Ps. gilvanii was pathogenic to açaí palms (Euterpe oleracea, E. precatoria), and oil palm (Elaeis guineensis), but not to banana (Musa paradisiaca var. pacovan) and rubber trees (Hevea brasiliensis). N. formicarum was not pathogenic to rubber trees but was pathogenic to other species tested. To our knowledge this is the first report of N. formicarum as a plant pathogen in the guarana plant, and Ps. gilvanii as novel plant pathogen capable of causing disease in important plant crops from tropical regions.

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Transcriptomic and metabolomic profiling reveals the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

10.21203/rs.3.rs-26873/v4 ◽

2020 ◽

Author(s):

Dejin Xie ◽

Lingyan Chen ◽

Chengcheng Zhou ◽

Muhammad Waqqas Khan Tarin ◽

Deming Yang ◽

...

Keyword(s):

Leaf Area ◽

Regulatory Mechanism ◽

Substantial Reduction ◽

Leaf Tissue ◽

Influential Factor ◽

Led Light ◽

Metabolomic Profiling ◽

Red Led ◽

Genes Encoding ◽

The Impact

Abstract Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. Results: The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin).Conclusion: These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.

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Education in the genomics era: Generating high-quality genome assemblies in university courses

GigaScience ◽

10.1093/gigascience/giaa058 ◽

2020 ◽

Vol 9 (6) ◽

Cited By ~ 3

Author(s):

Stefan Prost ◽

Sven Winter ◽

Jordi De Raad ◽

Raphael T F Coimbra ◽

Magnus Wolf ◽

...

Keyword(s):

Low Cost ◽

Genomic Data ◽

Master's Level ◽

Genome Data ◽

Sequencing Technologies ◽

Third Generation Sequencing ◽

University Courses ◽

Hands On ◽

Genome Assemblies ◽

High Quality Genome

Abstract Recent advances in genome sequencing technologies have simplified the generation of genome data and reduced the costs for genome assemblies, even for complex genomes like those of vertebrates. More practically oriented genomic courses can prepare university students for the increasing importance of genomic data used in biological and medical research. Low-cost third-generation sequencing technology, along with publicly available data, can be used to teach students how to process genomic data, assemble full chromosome-level genomes, and publish the results in peer-reviewed journals, or preprint servers. Here we outline experiences gained from 2 master's-level courses and discuss practical considerations for teaching hands-on genome assembly courses.

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High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-19-0280-a ◽

2020 ◽

Vol 33 (5) ◽

pp. 718-720

Author(s):

Karthi Natesan ◽

Ji Yeon Park ◽

Cheol-Woo Kim ◽

Dong Suk Park ◽

Young-Seok Kwon ◽

...

Keyword(s):

Downy Mildew ◽

De Novo ◽

Gc Content ◽

Comparative Genomic ◽

High Quality ◽

Sequencing Platform ◽

Peronospora Destructor ◽

Genomic Studies ◽

Genome Assemblies ◽

High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

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A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

GigaScience ◽

10.1093/gigascience/giz122 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 12

Author(s):

Sarah B Kingan ◽

Julie Urban ◽

Christine C Lambert ◽

Primo Baybayan ◽

Anna K Childers ◽

...

Keyword(s):

Invasive Species ◽

Genome Assembly ◽

De Novo ◽

Fragment Size ◽

High Quality ◽

De Novo Genome Assembly ◽

Lycorma Delicatula ◽

Long Read ◽

Genome Assemblies ◽

High Quality Genome

ABSTRACT Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

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Liftoff: accurate mapping of gene annotations

Bioinformatics ◽

10.1093/bioinformatics/btaa1016 ◽

2020 ◽

Author(s):

Alaina Shumate ◽

Steven L Salzberg

Keyword(s):

Reference Genome ◽

Supplementary Information ◽

Closely Related Species ◽

Protein Coding ◽

Human Reference Genome ◽

Sequence Identity ◽

Gene Annotations ◽

Genome Assemblies ◽

Average Sequence Identity ◽

High Quality Genome

Abstract Motivation Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. Results One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity. Availability and Implementation Liftoff can be installed via bioconda and PyPI. Additionally, the source code for Liftoff is available at https://github.com/agshumate/Liftoff Supplementary information Supplementary data are available at Bioinformatics online.

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Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

Frontiers in Plant Science ◽

10.3389/fpls.2021.625416 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nataliya V. Melnikova ◽

Elena N. Pushkova ◽

Ekaterina M. Dvorianinova ◽

Artemy D. Beniaminov ◽

Roman O. Novakovskiy ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Dioecious Species ◽

Male And Female ◽

Male Genome ◽

Oxford Nanopore ◽

Genome Assemblies ◽

First Time ◽

High Quality Genome ◽

Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

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Evaluation of Singlet Oxygen Scavenging Capacity of Peppermint (Mentha Piperita L.), Marjoram (Origanum Majorana L.), Rosemary (Rosmarinus Officinalis L.) And Sage (Salvia Officinalis L.) on Fatty Acid Photooxidation

Journal of Food Nutrition and Metabolism ◽

10.31487/j.jfnm.2019.03.03 ◽

2019 ◽

pp. 1-5

Author(s):

Mahdi Hajimohammadi ◽

Mona Pureisa ◽

Parisa Nosrati ◽

Samira Zanjirani ◽

...

Keyword(s):

Fatty Acids ◽

Oleic Acid ◽

Fatty Acid ◽

Singlet Oxygen ◽

Salvia Officinalis ◽

Mentha Piperita ◽

Oxygen Scavenger ◽

Salvia Officinalis L ◽

Rosmarinus Officinalis L ◽

Origanum Majorana

Lipid photooxidation is the undesirable chemical process in which singlet oxygen result in the peroxidation of fatty acids. In this study leaves methanolic extracts of peppermint (Mentha piperita L.), marjoram (Origanum majorana L.), rosemary (Rosmarinus officinalis L.) and sage (Salvia officinalis L.) were applied as the natural singlet oxygen scavenger. Amount of flavonoid compounds as the singlet oxygen scavenger agent in these plant species were decreased in the order of peppermint > marjoram> sage > rosemary. Also, The rate of quenching of singlet oxygen in the presence of 1,4-Diazabicyclo[2.2.2]octane (DABCO) as a well-known singlet oxygen scavenger and highly effective synthetic antioxidants in food industry such as Butylated hydroxyanisole (BHA), tert-Butylhydroquinone (TBHQ) and peppermint decreased in the order of peppermint > BHA > TBHQ > DABCO >. Furthermore, photooxidation of oleic acid as an unsaturated fatty acid in the presence of DABCO, peppermint, BHA and TBHQ indicated a preservation of 82.77%, 73.39%, 71.57% and 53.10% on peroxidation of oleic acid, respectively which reveals peppermint has an efficient role on protection of fatty acids from photooxidation. Practical application: In this study, it was confirmed that peppermint (Mentha piperita L.) performs an effective role in restricting or limitation of singlet oxygen generation and fatty acid photooxidation. In vitro study of scavenging effect of peppermint can correlate laboratory results to commercial scale up. However, this would also necessitate the progress of improved methods for the measurement of lipid peroxidation in vivo in the presence of peppermint.

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High-quality genome assemblies of male and female Populus x sibirica plants

Systems Biology and Bioinformatics (SBB-2020) : The Twelfth International Young Scientists School ◽

10.18699/sbb-2020-32 ◽

2020 ◽

Keyword(s):

High Quality ◽

Male And Female ◽

Genome Assemblies ◽

High Quality Genome

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ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

10.1101/2020.01.13.905240 ◽

2020 ◽

Author(s):

Lauren Coombe ◽

Vladimir Nikolić ◽

Justin Chu ◽

Inanc Birol ◽

René L. Warren

Keyword(s):

Reference Sequence ◽

Biological Research ◽

Closely Related Species ◽

Draft Assembly ◽

Short Read ◽

Sequencing Technologies ◽

Long Read ◽

Genome Assemblies ◽

High Quality Genome ◽

Reference Human Genome

AbstractSummaryThe ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short read assembly with a draft long read assembly, and a draft assembly with an assembly from a closely-related species. When scaffolding a human short read assembly using the reference human genome or a long read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using less than 11 GB of RAM. Compared to existing reference-guided assemblers, ntJoin generates highly contiguous assemblies faster and using less memory.Availability and implementationntJoin is written in C++ and Python, and is freely available at https://github.com/bcgsc/[email protected]

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