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来自秘鲁亚马逊地区的三种本地产油微藻转录组的从头组装和功能注释数据集。

Dataset of de novo assembly and functional annotation of the transcriptomes of three native oleaginous microalgae from the Peruvian Amazon.

作者信息

Cobos Marianela, Rodríguez Hicler N, Estela Segundo L, Castro Carlos G, Maddox J Dylan, Paredes Jae D, Saldaña Juan R, Tresierra Álvaro B, Castro Juan C

机构信息

Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Av. Abelardo Quiñones Km 2.5, San Juan Bautista, Loreto, 16006, Perú.

Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Psje. Los Paujiles S/N, San Juan Bautista, Loreto, 16000, Perú.

出版信息

Data Brief. 2020 Jun 21;31:105917. doi: 10.1016/j.dib.2020.105917. eCollection 2020 Aug.

DOI:10.1016/j.dib.2020.105917
PMID:32637510
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7327806/
Abstract

Microalgae are photosynthetic organisms with cosmopolitan distribution (i.e., marine, freshwater and terrestrial habitats) and possess a great diversity of species [1] and consequently an immense variation in biochemical compositions [2]. To date genomic information is available mainly from the model green microalga [3]. Here we provide the dataset of a de novo assembly and functional annotation of the transcriptomes of three native oleaginous microalgae from the Peruvian Amazon. Native oleaginous microalgae species sp., sp., and sp. were cultured in triplicate using Chu-10 medium with or without a source of nitrate (NaNO). Total RNA was purified, the cDNA libraries were constructed and sequenced as paired-end reads on an Illumina HiSeq™2500 platform. Transcriptomes were de novo assembled using Trinity v2.9.1. A total of 48,554 transcripts (range from 250 to 7966 bp; N50 = 1047) for sp., 108,126 transcripts (range from 250 to 8160 bp; N50 = 1090) for sp., and 77,689 transcripts (range from 250 to 8481 bp; N50 = 1281) for sp. were de novo assembled. Completeness of the assembled transcriptomes were evaluated with the Benchmarking Universal Single-Copy Orthologs (BUSCO) software v2/v3. Functional annotation of the assembled transcriptomes was conducted with TransDecoder v3.0.1 and the web-based platforms Kyoto Encyclopedia of Genes and Genomes (KEGG) Automatic Annotation Server (KAAS) and FunctionAnnotator. The raw reads were deposited into NCBI and are accessible via BioProject accession number PRJNA628966 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA628966) and Sequence Read Archive (SRA) with accession numbers: SRX8295665 (https://www.ncbi.nlm.nih.gov/sra/SRX8295665), SRX8295666 (https://www.ncbi.nlm.nih.gov/sra/SRX8295666), SRX8295667 (https://www.ncbi.nlm.nih.gov/sra/SRX8295667), SRX8295668 (https://www.ncbi.nlm.nih.gov/sra/SRX8295668), SRX8295669 (https://www.ncbi.nlm.nih.gov/sra/SRX8295669), and SRX8295670 (https://www.ncbi.nlm.nih.gov/sra/SRX8295670). Additionally, transcriptome shotgun assembly sequences and functional annotations are available via Discover Mendeley Data (https://data.mendeley.com/datasets/47wdjmw9xr/1).

摘要

微藻是具有全球分布（即海洋、淡水和陆地栖息地）的光合生物，拥有种类繁多的物种[1]，因此其生化组成也存在巨大差异[2]。迄今为止，基因组信息主要来自模式绿藻[3]。在此，我们提供了来自秘鲁亚马逊地区的三种本地产油微藻转录组的从头组装和功能注释数据集。本地产油微藻物种sp.、sp.和sp.使用添加或不添加硝酸盐源（NaNO）的Chu - 10培养基进行了三次重复培养。纯化了总RNA，构建了cDNA文库，并在Illumina HiSeq™2500平台上进行双端测序。使用Trinity v2.9.1对转录组进行从头组装。对于sp.，共从头组装了48,554个转录本（长度范围为250至7966 bp；N50 = 1047），对于sp.，组装了108,126个转录本（长度范围为250至8160 bp；N50 = 1090），对于sp.，组装了77,689个转录本（长度范围为250至8481 bp；N50 = 1281）。使用基准通用单拷贝直系同源物（BUSCO）软件v2/v3评估组装转录组的完整性。使用TransDecoder v3.0.1以及基于网络的京都基因与基因组百科全书（KEGG）自动注释服务器（KAAS）和功能注释器对组装转录组进行功能注释。原始读数已存入NCBI，可通过生物项目登录号PRJNA628966（https://www.ncbi.nlm.nih.gov/bioproject/PRJNA6289 / 66）和序列读取存档（SRA）获取，登录号分别为：SRX8295665（https://www.ncbi.nlm.nih.gov/sra/SRX8295665）、SRX8295666（https://www.ncbi.nlm.nih.gov/sra/SRX8295666）、SRX8295667（https://www.ncbi.nlm.nih.gov/sra/SRX8295667）、SRX8295668（https://www.ncbi.nlm.nih.gov/sra/SRX8295668）、SRX8295669（https://www.ncbi.nlm.nih.gov/sra/SRX8295669）和SRX8295670（https://www.ncbi.nlm.nih.gov/sra/SRX8295670）。此外，转录组鸟枪法组装序列和功能注释可通过Discover Mendeley Data（https://data.mendeley.com/datasets/47wdjmw9xr/1）获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/5d994443af00/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/d7863e391ae8/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/83b04cb43cf9/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/5d994443af00/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/d7863e391ae8/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/83b04cb43cf9/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f384/7327806/5d994443af00/gr3.jpg

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