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Draft genome sequence data of maqui (Aristotelia chilensis) and identification of SSR markers.

ABSTRACT: Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree, belonging to the Elaeocarpaceae family. Maqui fruit has high levels of antioxidant activity, which are due to elevated anthocyanin and polyphenol content. Here we describe a draft genome sequence data of maqui (A. chilensis). The genomic sequence datasets were obtained using Illumina NextSeq platform. Nucleotide sequences of raw reads and the assembled draft genome are available at NCBI's Sequence Read Archive as BioProject PRJNA544858. Also, a total of 210067 microsatellite or simple sequence repeat (SSR) markers were identified.

SUBMITTER: Bastias A

PROVIDER: S-EPMC6817651 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Draft genome sequence data of maqui (Aristotelia chilensis) and identification of SSR markers.

Bastías Adriana A Correa Francisco F Rojas Pamela P Martin Constanza C Pérez-Diaz Jorge J Yáñez Cristian C Cuevas Mara M Verdugo Ricardo R Sagredo Boris B

Data in brief 20190920

Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree, belonging to the Elaeocarpaceae family. Maqui fruit has high levels of antioxidant activity, which are due to elevated anthocyanin and polyphenol content. Here we describe a draft genome sequence data of maqui (A. chilensis). The genomic sequence datasets were obtained using Illumina NextSeq platform. Nucleotide sequences of raw reads and the assembled draft genome are available at NCBI's Sequence Read Archive ...[more]

PMID: 31673575

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Optimized aqueous extracts of maqui (Aristotelia chilensis) suitable for powder production.

Project description:The aim of this work was to obtain powders rich in bioactive compounds from maqui berry aqueous extracts by spray drying. First, the process parameters of the maqui aqueous extraction were optimized. The optimal operating conditions were found using an experimental Box-Behnken design with three factors: solvent/fruit ratio (2:1, 3.5:1 and 5:1), extraction temperature (25, 50 and 75 °C) and extraction time (30, 75 and 120 min). Soluble solids content, monomeric anthocyanin content (ACY), total polyphenol content (TPC) and antioxidant capacity in the liquid extracts were analyzed as key responses to find the optimal extraction conditions. Secondly, the best aqueous extract (solvent/fruit ratio = 2:1; extraction temperature = 75 °C and extraction time = 75 min) was subjected to spray drying. The effects of different drying adjuvants (maltodextrin, colloidal silicon dioxide, arabic gum, and microcrystalline cellulose) on the powders flow properties, the process yield (PY), the bioactive compounds content and the superficial color were studied. The product based on colloidal silicon dioxide presented the best powder properties: excellent flowability (α: 30.4 ± 0.7°, CI: 8.0 ± 1.7%), adequate moisture content (4.9 ± 0.3%), very good PY (70 ± 1%), high ACY (1528 ± 41 mg cy-3glu/100 g of powder) and TPC (3936 ± 132 mg GAE/100 g of powder), and a purple hue. This maqui powder offers valuable properties that allow its use, among other applications, as a functional ingredient, natural colorant and nutraceutical product.

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Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS).

Project description:Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

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Bioassay-Guided Isolation of Antioxidant and Cytoprotective Constituents from a Maqui Berry (Aristotelia chilensis) Dietary Supplement Ingredient As Markers for Qualitative and Quantitative Analysis.

Project description:Bioassay-guided phytochemical investigation of a commercially available maqui berry (Aristotelia chilensis) extract used in botanical dietary supplement products led to the isolation of 16 compounds, including one phenolic molecule, 1, discovered for the first time from a natural source, along with several known compounds, 2-16, including three substances not reported previously in A. chilensis, 2, 14, and 15. Each isolate was characterized by detailed analysis of NMR spectroscopic and HRESIMS data and tested for their in vitro hydroxyl radical scavenging and quinone-reductase inducing biological activities. A sensitive and accurate LC-DAD-MS method for the quantitative determination of the occurrence of six bioactive compounds, 6, 7, 10-12, and 14, was developed and validated using maqui berry isolates purified in the course of this study as authentic standards. The method presented can be utilized for dereplication efforts in future natural product research projects or to evaluate chemical markers for quality assurance and batch-to-batch standardization of this botanical dietary supplement component.

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Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry).

Project description:Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1). High-throughput sequencing of the genome of this tree uncovered an endogenous viral element, with a size of 7122 bp, corresponding to the complete genome of AcV1. Its sequence contains three open reading frames (ORFs): ORFs 1 and 2 shares 66%-73% amino acid similarity with members of the Caulimoviridae virus family, especially the Petunia vein clearing virus (PVCV), Petuvirus genus. ORF1 encodes a movement protein (MP); ORF2 a Reverse Transcriptase (RT) and a Ribonuclease H (RNase H) domain; and ORF3 showed no amino acid sequence similarity with any other known virus proteins. Analogous to other known endogenous pararetrovirus sequences (EPRVs), AcV1 is integrated in the genome of Maqui Berry and showed low viral transcriptional activity, which was detected by deep sequencing technology (DNA and RNA-seq). Phylogenetic analysis of AcV1 and other pararetroviruses revealed a closer resemblance with Petuvirus. Overall, our data suggests that AcV1 could be a new member of Caulimoviridae family, genus Petuvirus, and the first evidence of this kind of virus in a fruit plant.

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Lyophilized Maqui (Aristotelia chilensis) Berry Administration Suppresses High-Fat Diet-Induced Liver Lipogenesis through the Induction of the Nuclear Corepressor SMILE.

Project description:The liver is one of the first organs affected by accumulated ectopic lipids. Increased de novo lipogenesis and excessive triglyceride accumulation in the liver are hallmarks of nonalcoholic fatty liver disease (NAFLD) and are strongly associated with obesity, insulin resistance, and type 2 diabetes. Maqui dietary supplemented diet-induced obese mice showed better insulin response and decreased weight gain. We previously described that these positive effects of maqui are partially due to an induction of a brown-like phenotype in subcutaneous white adipose tissue that correlated with a differential expression of Chrebp target genes. In this work, we aimed to deepen the molecular mechanisms underlying the impact of maqui on the onset and development of the obese phenotype and insulin resistance focusing on liver metabolism. Our results showed that maqui supplementation decreased hepatic steatosis caused by a high-fat diet. Changes in the metabolic profile include a downregulation of the lipogenic liver X receptor (LXR) target genes and of fatty acid oxidation gene expression together with an increase in the expression of small heterodimer partner interacting leucine zipper protein (Smile), a corepressor of the nuclear receptor family. Our data suggest that maqui supplementation regulates lipid handling in liver to counteract the metabolic impact of a high-fat diet.

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Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz.

Project description:Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabilitation. However, the lack of genomic information of Acacia pachyceras hampers its genetic study and breeding process. We performed paired-end sequencing of A. pachyceras at a depth of 120X to obtain raw sequences of 108.9 GB with a per base quality >Q30. Filtered raw data was assembled into a fasta file of 4 GB. The assembled genomic sequences consisted of 901,755 single sequence repeats (SSRs). In total 11,596 primer pairs were designed against these SSR motifs. The data generated provides baseline genomic information about the species and formulates a base for further sequencing of A. pachyceras through PACBio and HiC technologies. The novel developed SSR markers will facilitate genetic diversity and conservation studies for Acacia species.

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