Dataset Information

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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Project description:BACKGROUND: Microsatellites or single sequence repeats (SSRs) are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. RESULTS: A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAG)n, (AGG)n and (AGC)n were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae). This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. CONCLUSION: Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum) are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as they are highly variable and easily amplifiable from different Phytophthora species.

Dataset Information

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

Publications

Draft genome sequence data of maqui <i>(Aristotelia chilensis)</i> and identification of SSR markers.

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