Bastías Adriana, Correa Francisco, Rojas Pamela, Almada Rubén, Muñoz Carlos, Sagredo Boris
Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile.
Facultad de Ingeniería, Universidad de Talca, Avenida Lircay s/n, Talca.
PLoS One. 2016 Jul 26;11(7):e0159825. doi: 10.1371/journal.pone.0159825. eCollection 2016.
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.
智利酒果（Aristotelia chilensis [Molina] Stunz）是一种原产于南美洲的小型雌雄异株树木，其果实可食用，具有极高的抗氧化能力和花青素含量。为了将智利酒果作为一种遗传资源加以保存，研究其遗传多样性至关重要。然而，其完整基因组尚不清楚，数据库中仅有少数基因序列。简单序列重复（SSR）标记具有中性、共显性、可重复性和高度变异性，有助于支持对智利酒果种群的遗传研究。通过利用454测序技术对智利酒果一个基因型的微卫星位点进行鉴定和表征，我们为该物种开发了一套SSR标记。共获得165,043条鸟枪法基因组序列，平均读长为387个碱基，覆盖了智利酒果基因组的64 Mb。读段被组装成4,832个重叠群，同时有98,546个读段保持为单拷贝，共产生103,378条一致的基因组序列。共鉴定出24,494个智利酒果SSR标记。其中，15,950个智利酒果SSR标记被归类为完美型。最常见的SSR基序是二核苷酸（31%），其次是四核苷酸（26%）和三核苷酸基序（24%）。基序AG/CT（28.4%）最为丰富，而基序AC（89 bp）最长。选择了11个多态性SSR标记，用于分析40个智利酒果基因型的群体。多态性信息含量（PIC）范围为0.117至0.82，平均为0.58。在智利酒果群体中未观察到显著的分组，呈现出随机交配的遗传结构。此外，我们还在智利酒果序列中预测了11150个推定基因和3个微小RNA（miRNA）。这些结果，包括来自智利酒果基因组DNA高通量下一代测序（NGS）的基因部分序列、一些miRNA和SSR标记，构成了对这一重要物种进行遗传和分子研究的首个平台。
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