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

Research output

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
Original languageEnglish
Title of host publicationVII ECOP - ISOP Joint Meeting
Pages246
Publication statusPublished - 2015
EventVII European Congress of Protistology - Sevilla
Duration: 4 Sep 20159 Sep 2015
http://eukref.org/event/vii-european-congress-of-protistology/

Conference

ConferenceVII European Congress of Protistology
CountrySpain
CitySevilla
Period4/09/159/09/15
Internet address

Fingerprint

DNA barcoding
Amoeba
transcriptome
genes
oases
habitats
Amoebozoa

Cite this

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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",
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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

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KW - филогения

KW - разнообразие

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