De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.

Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created...

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Autores principales:	Rachel A Schomaker, Jeffry L Dudycha
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/13b550a9950f462fb19ddaf0485abab8
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spelling	oai:doaj.org-article:13b550a9950f462fb19ddaf0485abab82021-11-25T06:19:14ZDe novo transcriptome assembly of the green alga Ankistrodesmus falcatus.1932-620310.1371/journal.pone.0251668https://doaj.org/article/13b550a9950f462fb19ddaf0485abab82021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251668https://doaj.org/toc/1932-6203Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.Rachel A SchomakerJeffry L DudychaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251668 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rachel A Schomaker Jeffry L Dudycha De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
description	Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.
format	article
author	Rachel A Schomaker Jeffry L Dudycha
author_facet	Rachel A Schomaker Jeffry L Dudycha
author_sort	Rachel A Schomaker
title	De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
title_short	De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
title_full	De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
title_fullStr	De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
title_full_unstemmed	De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.
title_sort	de novo transcriptome assembly of the green alga ankistrodesmus falcatus.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/13b550a9950f462fb19ddaf0485abab8
work_keys_str_mv	AT rachelaschomaker denovotranscriptomeassemblyofthegreenalgaankistrodesmusfalcatus AT jeffryldudycha denovotranscriptomeassemblyofthegreenalgaankistrodesmusfalcatus
_version_	1718413906748112896

De novo transcriptome assembly of the green alga Ankistrodesmus falcatus.

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