scholarly journals De novo assembly of a new Olea europaea genome accession using nanopore sequencing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Chunfu Lin ◽  
Huaigen Xin ◽  
...  
Keyword(s):  
Olea Europaea ◽  
De Novo ◽  
Draft Genome ◽  
Virgin Olive Oil ◽  
Gene Families ◽  
Extra Virgin Olive Oil ◽  
Genome Replication ◽  
Protein Coding ◽  
Oxford Nanopore ◽  
Olea Europaéa

AbstractOlive (Olea europaea L.) is internationally renowned for its high-end product, extra virgin olive oil. An incomplete genome of O. europaea was previously obtained using shotgun sequencing in 2016. To further explore the genetic and breeding utilization of olive, an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology. Seven different assembly strategies were used to assemble the final genome of 1.30 Gb, with contig and scaffold N50 sizes of 4.67 Mb and 42.60 Mb, respectively. This greatly increased the quality of the olive genome. We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C, and 53,518 protein-coding genes were predicted in the current assembly. Comparative genomics analyses, including gene family expansion and contraction, whole-genome replication, phylogenetic analysis, and positive selection, were performed. Based on the obtained high-quality olive genome, a total of nine gene families with 202 genes were identified in the oleuropein biosynthesis pathway, which is twice the number of genes identified from the previous data. This new accession of the olive genome is of sufficient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.

scholarly journals Sifat Histerisis Pada Konstanta Dielektrik dan Indeks Bias Minyak Zaitun Dengan Variasi Suhu

2018 ◽  
Vol 6 (1) ◽  
pp. 41 ◽  
Author(s):  
Luluk Mukarromah ◽  
Bowo Eko Cahyono ◽  
M. Misto
Keyword(s):  
Olive Oil ◽  
Olea Europaea ◽  
Virgin Olive Oil ◽  
Extra Virgin Olive Oil ◽  
Olea Europaéa

Minyak zaitun adalah minyak nabati yang diperoleh dari tanaman zaitun (olea europaea). Minyak zaitun dapat digunakan untuk memasak, bahan obat-obatan, dan sabun. Setiap bahan termasuk minyak zaitun memiliki sifat-sifat fisika dan besarnya sangat ditentukan oleh kondisi internal bahan tersebut. Penelitian ini dilakukan untuk mengetahui lebar kurva histerisis melalui pengukuran konstanta dielektrik dan indeks bias. Bahan yang diteliti berupa 3 jenis minyak zaitun. Penelitian ini menggunakan metode kapasitansimeter dan difraksi Fraunhofer celah ganda. Diketahui bahwa ketiga jenis minyak zaitun memiliki lebar kurva histerisis yang berbeda pada pengukuran konstanta dielektrik maupun indeks bias dengan variasi suhu. Hubungan antara nilai konstanta dielektrik terhadap suhu menunjukkan peningkatan, sedangkan untuk nilai indeks bias menunjukkan penurunan. Pada pengukuran konstanta dielektrik menunjukkan bahwa minyak zaitun virgin olive oil memiliki lebar kurva histerisis paling besar dibandingkan minyak zaitun extra virgin olive oil dan extra light olive oil. Hal ini menunjukkan bahwa minyak zaitun virgin olive oil memiliki kemampuan paling besar untuk menyimpan enegi termal. Sedangkan pada pengukuran indeks bias menunjukkan bahwa minyak zaitun extra virgin olive oil memiliki lebar kurva histerisis paling besar dibandingkan minyak zaitun extra light olive oil dan virgin olive oil,. Hal ini juga menunjukkan bahwa minyak zaitun extra virgin olive oil memiliki kemampuan paling besar untuk menyimpan enegi termal. Kata Kunci: Minyak zaitun, konstanta dielektrik, indeks bias, metode kapasitansimeter, metode difraksi Fraunhofer, kurva histerisis

scholarly journals Genetic Resources of Olea europaea L. in the Garda Trentino Olive Groves Revealed by Ancient Trees Genotyping and Parentage Analysis of Drupe Embryos

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1171
Author(s):  
Paula Moreno-Sanz ◽  
Luca Lombardo ◽  
Silvia Lorenzi ◽  
Franco Michelotti ◽  
Maria Stella Grando
Keyword(s):  
Genetic Resources ◽  
Olea Europaea ◽  
Virgin Olive Oil ◽  
Olive Tree ◽  
Extra Virgin Olive Oil ◽  
Parentage Analysis ◽  
Fruit Production ◽  
Olea Europaea L ◽  
Genetic Profiles ◽  
Olea Europaéa

The area of the Garda Lake within the Trentino province (north of Italy) is the northernmost part of Europe where the Mediterranean species Olea europaea L. is traditionally cultivated. ‘Casaliva’ is claimed as the main variety traditionally grown in the Garda Trentino area (GT) from which a world renowned niche extra virgin olive oil is produced. Since a dominant presence of ‘Casaliva’ would link the fruit set success and yield to a self-pollination compatibility system, a deep genetic survey of the olive tree population in the GT has been performed with the aim of establishing the actual varietal composition and of understanding from which pollen donor the ‘Casaliva’ olives originate. Forty-four different genetic profiles were observed among the 205 leaf samples collected from 106 ancient trees through the analysis of 20 nuclear microsatellite markers. The varietal composition in modern orchards was also explored and the vast majority of the additional 151 trees analyzed showed the same genotype as the ancient accessions of ‘Casaliva’. The results support the long historical link of ‘Casaliva’ with the GT and, besides a high varietal homogeneity, they also revealed the presence of olive genetic resources essential to fruit production. In fact, the parentage analysis of 550 embryos from drupes of ‘Casaliva’ evidenced that a cross-fertilization system is favored and a list of candidate cultivars most suitable as local pollinizers of ‘Casaliva’ was identified.

Extra virgin olive oil and related by-products (Olea europaea L.) as natural sources of phenolic compounds for abdominal pain relief in gastrointestinal disorders in rats

2020 ◽  
Vol 11 (12) ◽  
pp. 10423-10435
Author(s):  
Carmen Parisio ◽  
Elena Lucarini ◽  
Laura Micheli ◽  
Alessandra Toti ◽  
Maria Bellumori ◽  
...  
Keyword(s):  
Abdominal Pain ◽  
Phenolic Compounds ◽  
Pain Relief ◽  
Olea Europaea ◽  
Virgin Olive Oil ◽  
Extra Virgin Olive Oil ◽  
Gastrointestinal Disorders ◽  
Natural Sources ◽  
By Products ◽  
Olea Europaéa

Olea europaea-derived samples as natural source for abdominal pain relief in gastrointestinal disorders.

scholarly journals The genomes of two parasitic wasps that parasitize the diamondback moth

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Min Shi ◽  
Zhizhi Wang ◽  
Xiqian Ye ◽  
Hongqing Xie ◽  
Fei Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Diamondback Moth ◽  
Draft Genome ◽  
Gene Families ◽  
Detoxification Enzymes ◽  
Parasitic Wasps ◽  
Protein Coding ◽  
Wasp Species ◽  
Sequencing Platforms

Abstract Background Parasitic insects are well-known biological control agents for arthropod pests worldwide. They are capable of regulating their host’s physiology, development and behaviour. However, many of the molecular mechanisms involved in host-parasitoid interaction remain unknown. Results We sequenced the genomes of two parasitic wasps (Cotesia vestalis, and Diadromus collaris) that parasitize the diamondback moth Plutella xylostella using Illumina and Pacbio sequencing platforms. Genome assembly using SOAPdenovo produced a 178 Mb draft genome for C. vestalis and a 399 Mb draft genome for D. collaris. A total set that contained 11,278 and 15,328 protein-coding genes for C. vestalis and D. collaris, respectively, were predicted using evidence (homology-based and transcriptome-based) and de novo prediction methodology. Phylogenetic analysis showed that the braconid C. vestalis and the ichneumonid D. collaris diverged approximately 124 million years ago. These two wasps exhibit gene gains and losses that in some cases reflect their shared life history as parasitic wasps and in other cases are unique to particular species. Gene families with functions in development, nutrient acquisition from hosts, and metabolism have expanded in each wasp species, while genes required for biosynthesis of some amino acids and steroids have been lost, since these nutrients can be directly obtained from the host. Both wasp species encode a relative higher number of neprilysins (NEPs) thus far reported in arthropod genomes while several genes encoding immune-related proteins and detoxification enzymes were lost in both wasp genomes. Conclusions We present the annotated genome sequence of two parasitic wasps C. vestalis and D. collaris, which parasitize a common host, the diamondback moth, P. xylostella. These data will provide a fundamental source for studying the mechanism of host control and will be used in parasitoid comparative genomics to study the origin and diversification of the parasitic lifestyle.

scholarly journals Health Effects of Phenolic Compounds Found in Extra-Virgin Olive Oil, By-Products, and Leaf of Olea europaea L.

Nutrients ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1776 ◽  
Author(s):  
Annalisa Romani ◽  
Francesca Ieri ◽  
Silvia Urciuoli ◽  
Annalisa Noce ◽  
Giulia Marrone ◽  
...  
Keyword(s):  
Olive Oil ◽  
Olea Europaea ◽  
Biological Activities ◽  
Virgin Olive Oil ◽  
Extra Virgin Olive Oil ◽  
Green Technologies ◽  
Coronary Syndrome ◽  
Olea Europaea L ◽  
By Products ◽  
Olea Europaéa

Olea europaea L. fruit is a peculiar vegetal matrix containing high levels of fatty acids (98–99% of the total weight of extra-virgin olive oil, EVOO) and low quantities (1–2%) of phenolics, phytosterols, tocopherols, and squalene. Among these minor components, phenolics are relevant molecules for human health. This review is focused on their beneficial activity, in particular of hydroxytyrosol (HT), oleuropein (OLE), oleocanthal (OLC), and lignans found in EVOO, olive oil by-products and leaves. Specifically, the cardioprotective properties of the Mediterranean diet (MD) related to olive oil consumption, and the biological activities of polyphenols recovered from olive oil by-products and leaves were described. Recent European projects such as EPIC (European Prospective Investigation into Cancer and Nutrition) and EPICOR (long-term follow-up of antithrombotic management patterns in acute coronary syndrome patients) have demonstrated the functional and preventive activities of EVOO showing the relation both between cancer and nutrition and between consumption of EVOO, vegetables, and fruit and the incidence of coronary heart disease. The data reported in this review demonstrate that EVOO, one of the pillars of the MD, is the main product of Olea europaea L. fruits; leaves and by-products are secondary but precious products from which bioactive compounds can be recovered by green technologies and reused for food, agronomic, nutraceutical, and biomedical applications according to the circular economy strategy.

scholarly journals Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Robert M. Nowak ◽  
Jan P. Jastrzębski ◽  
Wiktor Kuśmirek ◽  
Rusłan Sałamatin ◽  
Małgorzata Rydzanicz ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Model Organism ◽  
Gene Families ◽  
Hymenolepis Diminuta ◽  
Quality Data ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Mate Pair ◽  
Oxford Nanopore

AbstractDespite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.

scholarly journals Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India

2021 ◽  
Author(s):  
VISHNU PRASOODANAN P K ◽  
Shruti S. Menon ◽  
Rituja Saxena ◽  
Prashant Waiker ◽  
Vineet K Sharma
Keyword(s):  
Hot Springs ◽  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Central India ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Protein Coding ◽  
Protein Coding Genes

Discovery of novel thermophiles has shown promising applications in the field of biotechnology. Due to their thermal stability, they can survive the harsh processes in the industries, which make them important to be characterized and studied. Members of Anoxybacillus are alkaline tolerant thermophiles and have been extensively isolated from manure, dairy-processed plants, and geothermal hot springs. This article reports the assembled data of an aerobic bacterium Anoxybacillus sp. strain MB8, isolated from the Tattapani hot springs in Central India, where the 16S rRNA gene shares an identity of 97% (99% coverage) with Anoxybacillus kamchatkensis strain G10. The de novo assembly and annotation performed on the genome of Anoxybacillus sp. strain MB8 comprises of 2,898,780 bp (in 190 contigs) with a GC content of 41.8% and includes 2,976 protein-coding genes,1 rRNA operon, 73 tRNAs, 1 tm-RNA and 10 CRISPR arrays. The predicted protein-coding genes have been classified into 21 eggNOG categories. The KEGG Automated Annotation Server (KAAS) analysis indicated the presence of assimilatory sulfate reduction pathway, nitrate reducing pathway, and genes for glycoside hydrolases (GHs) and glycoside transferase (GTs). GHs and GTs hold widespread applications, in the baking and food industry for bread manufacturing, and in the paper, detergent and cosmetic industry. Hence, Anoxybacillus sp. strain MB8 holds the potential to be screened and characterized for such commercially relevant enzymes.

Sign in / Sign up

Export Citation Format

Share Document