scholarly journals Assessing Diversity in the Camelina Genus Provides Insights into the Genome Structure of Camelina sativa

2020 ◽  
Vol 10 (4) ◽  
pp. 1297-1308 ◽  
Author(s):  
Raju Chaudhary ◽  
Chu Shin Koh ◽  
Sateesh Kagale ◽  
Lily Tang ◽  
Siu Wah Wu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Allelic Variation ◽  
Genome Structure ◽  
Genotyping By Sequencing ◽  
Camelina Sativa ◽  
Oilseed Crop ◽  
Evolutionary Trajectory ◽  
Russian Region ◽  
Limited Genetic Diversity ◽  
Brassicaceae Family

Camelina sativa (L.) Crantz an oilseed crop of the Brassicaceae family is gaining attention due to its potential as a source of high value oil for food, feed or fuel. The hexaploid domesticated C. sativa has limited genetic diversity, encouraging the exploration of related species for novel allelic variation for traits of interest. The current study utilized genotyping by sequencing to characterize 193 Camelina accessions belonging to seven different species collected primarily from the Ukrainian-Russian region and Eastern Europe. Population analyses among Camelina accessions with a 2n = 40 karyotype identified three subpopulations, two composed of domesticated C. sativa and one of C. microcarpa species. Winter type Camelina lines were identified as admixtures of C. sativa and C. microcarpa. Eighteen genotypes of related C. microcarpa unexpectedly shared only two subgenomes with C. sativa, suggesting a novel or cryptic sub-species of C. microcarpa with 19 haploid chromosomes. One C. microcarpa accession (2n = 26) was found to comprise the first two subgenomes of C. sativa suggesting a tetraploid structure. The defined chromosome series among C. microcarpa germplasm, including the newly designated C. neglecta diploid née C. microcarpa, suggested an evolutionary trajectory for the formation of the C. sativa hexaploid genome and re-defined the underlying subgenome structure of the reference genome.

scholarly journals Genome improvement and genetic map construction for Aethionema arabicum, the first divergent branch in the Brassicaceae family

2019 ◽  
Author(s):  
Thu-Phuong Nguyen ◽  
Cornelia Mühlich ◽  
Setareh Mohammadin ◽  
Erik van den Bergh ◽  
Adrian E. Platts ◽  
...  
Keyword(s):  
Genetic Map ◽  
Reference Genome ◽  
Genotyping By Sequencing ◽  
Sister Group ◽  
Sequencing Data ◽  
Wide Range ◽  
Long Read ◽  
Genome Draft ◽  
Draft Version ◽  
Brassicaceae Family

AbstractBackgroundThe genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum. Secondly, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other.ResultsWe started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called bases, assembled into 2,883 scaffolds. The N50 (10.3 MB) represents an 80-fold over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups.ConclusionsWe show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum. They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.

scholarly journals Genome-edited Camelina sativa with a unique fatty acid content and its potential impact on ecosystems

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Katharina Kawall
Keyword(s):  
Fatty Acid ◽  
Genome Editing ◽  
Defense Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Fatty Acid Content ◽  
Camelina Sativa ◽  
Nutritional Composition ◽  
Oilseed Crop ◽  
Biotic And Abiotic Stress ◽  
Multiple Copies

Abstract‘Genome editing’ is intended to accelerate modern plant breeding enabling a much faster and more efficient development of crops with improved traits such as increased yield, altered nutritional composition, as well as resistance to factors of biotic and abiotic stress. These traits are often generated by site-directed nuclease-1 (SDN-1) applications that induce small, targeted changes in the plant genomes. These intended alterations can be combined in a way to generate plants with genomes that are altered on a larger scale than it is possible with conventional breeding techniques. The power and the potential of genome editing comes from its highly effective mode of action being able to generate different allelic combinations of genes, creating, at its most efficient, homozygous gene knockouts. Additionally, multiple copies of functional genes can be targeted all at once. This is especially relevant in polyploid plants such as Camelina sativa which contain complex genomes with multiple chromosome sets. Intended alterations induced by genome editing have potential to unintentionally alter the composition of a plant and/or interfere with its metabolism, e.g., with the biosynthesis of secondary metabolites such as phytohormones or other biomolecules. This could affect diverse defense mechanisms and inter-/intra-specific communication of plants having a direct impact on associated ecosystems. This review focuses on the intended alterations in crops mediated by SDN-1 applications, the generation of novel genotypes and the ecological effects emerging from these intended alterations. Genome editing applications in C. sativa are used to exemplify these issues in a crop with a complex genome. C. sativa is mainly altered in its fatty acid biosynthesis and used as an oilseed crop to produce biofuels.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Camelina (Camelina sativa L. Crantz) Crop Performance, Insect Pollinators, and Pollen Dispersal in the Northeastern US

2019 ◽  
Author(s):  
Richard Rizzitello ◽  
Chuan-Jie Zhang ◽  
Carol Auer
Keyword(s):  
Gene Flow ◽  
Honey Bees ◽  
Pollen Dispersal ◽  
Camelina Sativa ◽  
Genetically Engineered ◽  
Oilseed Crop ◽  
Crop Failure ◽  
Long Distance ◽  
Insect Visitation ◽  
Pollinating Insects

AbstractCamelina sativa (camelina) is an oilseed crop in the Brassicaceae that has been genetically engineered for the production of biofuels, dietary supplements, and other industrial compounds. Cultivation in North America is both recent and limited, so there are gaps in knowledge regarding yield, weed competition, and pollen-mediated gene flow. For these experiments, camelina ‘SO-40’ was grown for three years without weed control. Spring-sown camelina was harvested at 80-88 days with ∼1200 growing degree days (GDD) with yields of 425-508 kg/hectare. Camelina yields were the same with or without weeds, showing competitive ability in low-management conditions. Crop failure in 2015 was associated with delayed rainfall and above-average temperatures after seeding. Camelina flowers attracted pollinating insects from the Hymenoptera, Diptera, Lepidoptera, and Coleoptera. Hymenoptera included honey bees (Apis melifera), mining bees (Andrenidae), sweat bees (Halictidae), bumble bees (Bombus spp.) and leaf cutter bees (Megachilidae). Insect visitation on camelina flowers was associated with modest increases in seed yield. Honey bees comprised 28-33% of all pollinators and were shown to carry camelina pollen on their legs. Air sampling showed that wind-blown pollen was present at low concentrations at 9 m beyond the edges of the field. These experiments demonstrated for the first time that camelina pollen dispersal could occur through honey bees or wind, although bee activity would likely be more significant for long-distance gene flow.

scholarly journals Physical and chemical characteristics and fatty acids composition of seeds oil isolated from Camelina sativa (L) cultivated in Mongolia

2014 ◽  
Vol 14 ◽  
pp. 80-83 ◽  
Author(s):  
B Chantsalnyam ◽  
Ch Otgonbayar ◽  
O Enkhtungalag ◽  
P Odonmajig
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Unsaturated Fatty Acids ◽  
Mineral Elements ◽  
Camelina Sativa ◽  
Chemical Characteristics ◽  
Oilseed Crop ◽  
Fatty Acids Composition ◽  
Physical And Chemical Characteristics ◽  
Physical And Chemical

Camelina sativa L is a cruciferous oilseed plant. This plant is cultivated as an oilseed crop mainly in Europe and in North America and over the past years the cultivation has arranged in our country. The analyzed oil is obtained from the seeds of Camelina sativa L, growing in Bornuur, Tuv province. The goal of this study was to determine the physical and chemical characteristics and fatty acids composition of Camelina sativa L seed oil cultivated in Mongolia. According to our analysis total lipid was determined 38.52 %, moisture 4.80 % and total mineral elements 4.02 %, respectively. Mineral elements in Camelina sativa L seeds contain calcium (0.56 %), phosphorous (1.22 %), potassium (1.39 %), magnesium (0.53 %) in dominated amounts; iron, zinc, manganese and copper in trace amounts. Eight nonessential amino acids in seeds of this plant with total amount of 75.9 % were identified; phenylalanine was detected in highest amount among the all identified amino acids, while lysine, tryptophan and arginine are followed. The following characteristics in Camelina sativa seeds oil were determined. The refractive index was 1.4774 at 20°C, the peroxide value of fresh oil was 0.03 meq H2O2 /kg, saponification value 185.8 mg KOH/g, iodine value 143.33 g J2 and acidic value 6.27 mg KOH /g. Carotenoid was determined as 16.77 mg %, by spectrometry in Camelina sativa seeds oil. The analysis of fatty acids composition showed that there are 12.5 % saturated and 87.5 % unsaturated fatty acids. In particular, oleic acid (C18:1) 14.0 %, linoleic acid (C18:2) 9.0 %, α-linolenic acid (C18:3) 10.5 % and gondoic acid (C20:1) 32.8 %, were composed the major part of unsaturated fatty acids. DOI: http://dx.doi.org/10.5564/mjc.v14i0.205 Mongolian Journal of Chemistry 14 (40), 2013, p80-83

scholarly journals Results of Сamelina oil assessment

2020 ◽  
Author(s):  
E.L. Turina ◽  
◽  
S.G. Efimenko ◽  
Yu.A. Kornev ◽  
A.P. Liksutina ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Methyl Esters ◽  
Camelina Sativa ◽  
Biologically Active ◽  
Homogeneous Catalyst ◽  
Gas Liquid Chromatography ◽  
Oilseed Crop ◽  
Omega 3 ◽  
Alkaline Catalyst ◽  
The Crimea

Camelina sativa (L.) Crantz – is an annual oilseed crop in the family Brassicaceae. The aim of the research was to study oil obtained from camelina seeds cultivated in the Crimea. Determination of fatty acid composition was carried out on the gas chromatograph “Хроматэк – Кристалл 5000” (Hromatek - Crystal 5000); automatic dosing unit ДАЖ-2М (DAJ- 2M); capillary column SolGelWax 30m × 0.25 mm × 0.5 μm; carrier gas – helium; speed – 22 centimeters per second; programming temperature –178–230 °С. The preparation of fatty acid methyl esters (FAMEs) using gas-liquid chromatography (GC) was performed in line with the methodology. The content of biologically active substances (tocopherols) in Camelina sativa oil was carried out using thin-layer chromatography (TLC) and spectroscopy. To obtain biofuel, we used the transesterification of triglyceride (or triacylglycerols) of camelina oil with methyl alcohol using potassium hydroxide (or sodium) as a homogeneous catalyst, as well as active metal oxides or enzymes (regiospecific lipase) as heterogeneous catalysts. Camelina sativa oil, obtained from false flax cultivated in the Crimea, should be used, first of all, to ensure healthy, dietary and therapeutic nutrition of the locals and tourists. Since, depending on the variety and the amount of precipitation, it contains 17.89-19.66% of linoleic acid; 33.02-37.06% of linolenic acid; not more than 3.05% of erucic acid. Furthermore, the ratio of omega-3 to omega-6 fatty acids varies from 1.7: 1.0 to 2.2: 1.0 even in wet years. The oil from the winter camelina seeds (‘Penzyak’ variety) in its composition and properties is suitable for the synthesis of biodiesel by the methanolysis reaction using a homogeneous alkaline catalyst. The physical and chemical properties of the obtained biodiesel are similar to those of sunflower or rapeseed oils.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

scholarly journals Oil from transgenic Camelina sativa containing over 25 % n-3 long-chain PUFA as the major lipid source in feed for Atlantic salmon (Salmo salar)

2018 ◽  
Vol 119 (12) ◽  
pp. 1378-1392 ◽  
Author(s):  
Mónica B. Betancor ◽  
Keshuai Li ◽  
Valentin S. Bucerzan ◽  
Matthew Sprague ◽  
Olga Sayanova ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Supply And Demand ◽  
Camelina Sativa ◽  
Genetically Engineered ◽  
Oilseed Crop ◽  
Camelina Oil ◽  
Chain Pufa ◽  
Lipid Source ◽  
Long Chain

AbstractFacing a bottleneck in the growth of aquaculture, and a gap in the supply and demand of the highly beneficial n-3 long-chain PUFA (LC-PUFA), sustainable alternatives to traditional marine-based feeds are required. Therefore, in the present trial, a novel oil obtained from a genetically engineered oilseed crop, Camelina sativa, that supplied over 25 % n-3 LC-PUFA was tested as a sole dietary-added lipid source in Atlantic salmon (Salmo salar) feed. Three groups of fish were fed three experimental diets for 12 weeks with the same basal composition and containing 20 % added oil supplied by either a blend of fish oil and rapeseed oil (1:3) (COM) reflecting current commercial formulations, wild-type Camelina oil (WCO) or the novel transgenic Camelina oil (TCO). There were no negative effects on the growth, survival rate or health of the fish. The whole fish and flesh n-3 LC-PUFA levels were highest in fish fed TCO, with levels more than 2-fold higher compared with those of fish fed the COM and WCO diets, respectively. Diet TCO had no negative impacts on the evaluated immune and physiological parameters of head kidney monocytes. The transcriptomic responses of liver and mid-intestine showed only mild effects on metabolism genes. Overall, the results clearly indicated that the oil from transgenic Camelina was highly efficient in supplying n-3 LC-PUFA providing levels double that obtained with a current commercial standard, and similar to those a decade ago before substantial dietary fishmeal and oil replacement.

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