scholarly journals First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis

2018 ◽  
Author(s):  
Luana Ferreira Afonso ◽  
Danielle Amaral ◽  
Marcela Uliano-Silva ◽  
André Luiz Quintanilha Torres ◽  
Daniel Reis Simas ◽  
...  
Keyword(s):  
De Novo ◽  
Pfam Domain ◽  
Draft Genome ◽  
Atlantic Rainforest ◽  
Volatile Fraction ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
Limonene Synthase ◽  
Molecular Bases

BackgroundProtium species produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.ResultsHere we present (i) the first draft genome of an endemic tree of the Brazil’s Atlantic Rainforest (Mata Atlântica), Protium kleinii Cuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resin’s volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenes α-terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resin’s volatile fraction identified four monoterpenes: terpinolene, limonene, α-pinene and α-phellandrene.ConclusionThese results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.

scholarly journals Characterization of Histone Genes from the Bivalve Lucina Pectinata

2018 ◽  
Vol 15 (10) ◽  
pp. 2170 ◽  
Author(s):  
Ingrid Montes-Rodríguez ◽  
Yesenia Rodríguez-Pou ◽  
Ricardo González-Méndez ◽  
Juan Lopez-Garriga ◽  
Alexander Ropelewski ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Aquatic Organisms ◽  
Histone Genes ◽  
Coding Region ◽  
Lucina Pectinata ◽  
Coding Regions ◽  
Semiconductor Sequencing ◽  
Amino Acid Sequence Conservation

Lucina pectinata is a clam that lives in sulfide-rich environments and houses intracellular sulfide-oxidizing endosymbionts. To identify new Lucina pectinata proteins, we produced libraries for genome and transcriptome sequencing and assembled them de novo. We searched for histone-like sequences using the Lucina pectinata histone H3 partial nucleotide sequence against our previously described genome assembly to obtain the complete coding region and identify H3 coding sequences from mollusk sequences in Genbank. Solen marginatus histone nucleotide sequences were used as query sequences using the genome and transcriptome assemblies to identify the Lucina pectinata H1, H2A, H2B and H4 genes and mRNAs and obtained the complete coding regions of the five histone genes by RT-PCR combined with automated Sanger DNA sequencing. The amino acid sequence conservation between the Lucina pectinata and Solen marginatus histones was: 77%, 93%, 83%, 96% and 97% for H1, H2A, H2B, H3 and H4, respectively. As expected, the H3 and H4 proteins were the most conserved and the H1 proteins were most similar to H1′s from aquatic organisms like Crassostrea gigas, Aplysia californica, Mytilus trossulus and Biomphalaria glabrata. The Lucina pectinata draft genome and transcriptome assemblies, obtained by semiconductor sequencing, were adequate for identification of conserved proteins as evidenced by our results for the histone genes.

scholarly journals Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44911 ◽  
Author(s):  
Tingjuan Gao ◽  
Jitka Petrlova ◽  
Wei He ◽  
Thomas Huser ◽  
Wieslaw Kudlick ◽  
...  
Keyword(s):  
De Novo

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

scholarly journals De Novo Assembly and Characterization of the Xenocatantops brachycerus Transcriptome

2018 ◽  
Vol 19 (2) ◽  
pp. 520 ◽  
Author(s):  
Le Zhao ◽  
Xinmei Zhang ◽  
Zhongying Qiu ◽  
Yuan Huang
Keyword(s):  
De Novo Assembly ◽  
De Novo

scholarly journals Prenatal diagnosis and molecular cytogenetic characterization of a de novo duplication of 15q24.3-q26.1

2018 ◽  
Vol Volume 11 ◽  
pp. 77-80 ◽  
Author(s):  
Isabel Ochando ◽  
Melanie Cristine Alonzo Martínez ◽  
Ana María Serrano ◽  
Antonio Urbano ◽  
Eduardo Cazorla ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
De Novo ◽  
Molecular Cytogenetic ◽  
Cytogenetic Characterization

scholarly journals Ultrasound evaluation of access complications: Thrombosis, aneurysms, pseudoaneurysms and infections

2021 ◽  
pp. 112972982110180
Author(s):  
Mario Meola ◽  
Antonio Marciello ◽  
Gianfranco Di Salle ◽  
Ilaria Petrucci
Keyword(s):  
Vascular Access ◽  
Pulse Wave ◽  
De Novo ◽  
Late Complications ◽  
Prosthesis Infection ◽  
Ultrasound Evaluation ◽  
Access Complications ◽  
Vein Stenosis ◽  
Post Implantation

Arteriovenous fistula (AVF) complications are classified based on fistula outcomes. This review aims to update colour Doppler (CD) and pulse wave Doppler (PWD) roles in managing early and late complications of the native and prosthetic AVF. Vascular access (VA) failure occurs because inflow or outflow stenosis activates Wirchow’s triad inducing thrombosis. Therefore, the diagnosis of the tributary artery and outgoing vein stenosis will be the first topic considered. Post-implantation complications occur from the inability to achieve AVF maturation and dialysis suitability due to inflow/outflow stenosis. Late stenosis is usually a sequence of early defects repaired to maintain patency. Less frequently, in the mature AVF or graft, complications are acquired ‘de novo’. They derive either from incorrect management of vascular access (haematoma, pseudoaneurysm, prosthesis infection) or wall pathologies (aneurysm, myxoid valve degeneration, kinking, coiling, abnormal dilation from defects of elastic structures). High-resolution transducers (10–20 MHz) allow the characterization of the wall damage, haemodynamic dysfunctions, early and late complications even if phlebography remains the gold standard for the diagnosis for its sensitivity and specificity.

scholarly journals Characterization of Basil Volatile Fraction and Study of Its Agronomic Variation by ASCA

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3842
Author(s):  
Alessandro D’Alessandro ◽  
Daniele Ballestrieri ◽  
Lorenzo Strani ◽  
Marina Cocchi ◽  
Caterina Durante
Keyword(s):  
Food Industry ◽  
Principal Component ◽  
Component Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Volatile Fraction ◽  
Combined Effects ◽  
A Posteriori ◽  
Aroma Profile ◽  
Simultaneous Component Analysis

Basil is a plant known worldwide for its culinary and health attributes. It counts more than a hundred and fifty species and many more chemo-types due to its easy cross-breeds. Each species and each chemo-type have a typical aroma pattern and selecting the proper one is crucial for the food industry. Twelve basil varieties have been studied over three years (2018–2020), as have four different cuts. To characterize the aroma profile, nine typical basil flavour molecules have been selected using a gas chromatography–mass spectrometry coupled with an olfactometer (GC–MS/O). The concentrations of the nine selected molecules were measured by an ultra-fast CG e-nose and Principal Component Analysis (PCA) was applied to detect possible differences among the samples. The PCA results highlighted differences between harvesting years, mainly for 2018, whereas no observable clusters were found concerning varieties and cuts, probably due to the combined effects of the investigated factors. For this reason, the ANOVA Simultaneous Component Analysis (ASCA) methodology was applied on a balanced a posteriori designed dataset. All the considered factors and interactions were statistically significant (p < 0.05) in explaining differences between the basil aroma profiles, with more relevant effects of variety and year.

scholarly journals Identification and molecular characterization of de novo translocation t(8;14)(q22.3;q13) associated with a vascular and tissue overgrowth syndrome

2001 ◽  
Vol 95 (3-4) ◽  
pp. 183-188 ◽  
Author(s):  
Q. Wang ◽  
A.A. Timur ◽  
P. Szafranski ◽  
A. Sadgephour ◽  
V. Jurecic ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
De Novo ◽  
Overgrowth Syndrome ◽  
De Novo Translocation
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