Amoebozoa-specific genes as potential DNA barcodes to study environmental diversity of amoebae

Результат исследований: Публикации в книгах, отчётах, сборниках, трудах конференцийстатья в сборнике материалов конференциинаучнаярецензирование

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Implication of metagenomic approaches show that the amount of unexplored diversity in the environmental appears to be enormous, providing a background to the term “the dark matter of life”. Amoebozoa are among the groups that are numerous in all kinds of habitats, but rarely represent more than several percent of the total number of sequences when routine DNA barcodes (SSU gene, Cox I gene) are used to study environmental diversity. To explore cryptic diversity of Amoebozoa in the natural habitats we attempted to find Amoebozoa-specific genes and gene families for future application as a DNA barcodes in environmental studies. For this we analyze the transcriptomes of 11 Amoebozoa species represented in MMETSP database (marinemicroeukaryotes.org). We assembled them de novo using Velvet assembler based on de Bruijn graphs optimization algorithm. The preliminary assemblies at the output of Velvet were forwarded to Oases transcriptome assembler. To evaluate quality of transcriptome assemblies we used both QUAST
Язык оригиналаанглийский
Название основной публикацииVII ECOP - ISOP Joint Meeting
Страницы246
СостояниеОпубликовано - 2015
СобытиеVII European Congress of Protistology - Sevilla, Испания
Продолжительность: 4 сен 20159 сен 2015
http://eukref.org/event/vii-european-congress-of-protistology/

Конференция

КонференцияVII European Congress of Protistology
СтранаИспания
ГородSevilla
Период4/09/159/09/15
Адрес в сети Интернет

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    @inproceedings{d3d1c1c990f2448c878971d9b10555f3,
    title = "Amoebozoa-specific genes as potential DNA barcodes to study environmental diversity of amoebae",
    abstract = "Implication of metagenomic approaches show that the amount of unexplored diversity in the environmental appears to be enormous, providing a background to the term “the dark matter of life”. Amoebozoa are among the groups that are numerous in all kinds of habitats, but rarely represent more than several percent of the total number of sequences when routine DNA barcodes (SSU gene, Cox I gene) are used to study environmental diversity. To explore cryptic diversity of Amoebozoa in the natural habitats we attempted to find Amoebozoa-specific genes and gene families for future application as a DNA barcodes in environmental studies. For this we analyze the transcriptomes of 11 Amoebozoa species represented in MMETSP database (marinemicroeukaryotes.org). We assembled them de novo using Velvet assembler based on de Bruijn graphs optimization algorithm. The preliminary assemblies at the output of Velvet were forwarded to Oases transcriptome assembler. To evaluate quality of transcriptome assemblies we used both QUAST",
    keywords = "протистология, филогения, разнообразие",
    author = "N. Bondarenko and A. Bondarenko and A. Smirnov",
    year = "2015",
    language = "English",
    pages = "246",
    booktitle = "VII ECOP - ISOP Joint Meeting",

    }

    Bondarenko, N, Bondarenko, A & Smirnov, A 2015, Amoebozoa-specific genes as potential DNA barcodes to study environmental diversity of amoebae. в VII ECOP - ISOP Joint Meeting. стр. 246, VII European Congress of Protistology, Sevilla, Испания, 4/09/15.

    Amoebozoa-specific genes as potential DNA barcodes to study environmental diversity of amoebae. / Bondarenko, N.; Bondarenko, A.; Smirnov, A.

    VII ECOP - ISOP Joint Meeting. 2015. стр. 246.

    Результат исследований: Публикации в книгах, отчётах, сборниках, трудах конференцийстатья в сборнике материалов конференциинаучнаярецензирование

    TY - GEN

    T1 - Amoebozoa-specific genes as potential DNA barcodes to study environmental diversity of amoebae

    AU - Bondarenko, N.

    AU - Bondarenko, A.

    AU - Smirnov, A.

    PY - 2015

    Y1 - 2015

    N2 - Implication of metagenomic approaches show that the amount of unexplored diversity in the environmental appears to be enormous, providing a background to the term “the dark matter of life”. Amoebozoa are among the groups that are numerous in all kinds of habitats, but rarely represent more than several percent of the total number of sequences when routine DNA barcodes (SSU gene, Cox I gene) are used to study environmental diversity. To explore cryptic diversity of Amoebozoa in the natural habitats we attempted to find Amoebozoa-specific genes and gene families for future application as a DNA barcodes in environmental studies. For this we analyze the transcriptomes of 11 Amoebozoa species represented in MMETSP database (marinemicroeukaryotes.org). We assembled them de novo using Velvet assembler based on de Bruijn graphs optimization algorithm. The preliminary assemblies at the output of Velvet were forwarded to Oases transcriptome assembler. To evaluate quality of transcriptome assemblies we used both QUAST

    AB - Implication of metagenomic approaches show that the amount of unexplored diversity in the environmental appears to be enormous, providing a background to the term “the dark matter of life”. Amoebozoa are among the groups that are numerous in all kinds of habitats, but rarely represent more than several percent of the total number of sequences when routine DNA barcodes (SSU gene, Cox I gene) are used to study environmental diversity. To explore cryptic diversity of Amoebozoa in the natural habitats we attempted to find Amoebozoa-specific genes and gene families for future application as a DNA barcodes in environmental studies. For this we analyze the transcriptomes of 11 Amoebozoa species represented in MMETSP database (marinemicroeukaryotes.org). We assembled them de novo using Velvet assembler based on de Bruijn graphs optimization algorithm. The preliminary assemblies at the output of Velvet were forwarded to Oases transcriptome assembler. To evaluate quality of transcriptome assemblies we used both QUAST

    KW - протистология

    KW - филогения

    KW - разнообразие

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