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Exploring the unmapped DNA and RNA reads in a songbird genome. / Laine, Veronika N (Corresponding author); Gossmann, Toni I; van Oers, Kees; Visser, Marcel E; Groenen, Martien A M.

In: BMC Genomics, Vol. 20, No. 1, 19, 08.01.2019.

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Laine, Veronika N ; Gossmann, Toni I ; van Oers, Kees ; Visser, Marcel E ; Groenen, Martien A M. / Exploring the unmapped DNA and RNA reads in a songbird genome. In: BMC Genomics. 2019 ; Vol. 20, No. 1.

BibTeX

@article{bd3215164459417fa8d0f250dd4f34e7,
title = "Exploring the unmapped DNA and RNA reads in a songbird genome",
abstract = "BACKGROUND: A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.RESULTS: Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.CONCLUSIONS: Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.",
keywords = "international",
author = "Laine, {Veronika N} and Gossmann, {Toni I} and {van Oers}, Kees and Visser, {Marcel E} and Groenen, {Martien A M}",
note = "6685, AnE; Data Archiving: Data archived at: SRA repository. We used data already available in SRA repository (samples in BioProject PRJNA208335) and also generated new sequence datasets: SRA accession for blood RNA SRR7540238 and GenBank accession number for the assembled mitochondria MH638304.",
year = "2019",
month = "1",
day = "8",
doi = "10.1186/s12864-018-5378-2",
language = "English",
volume = "20",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

RIS

TY - JOUR

T1 - Exploring the unmapped DNA and RNA reads in a songbird genome

AU - Laine, Veronika N

AU - Gossmann, Toni I

AU - van Oers, Kees

AU - Visser, Marcel E

AU - Groenen, Martien A M

N1 - 6685, AnE; Data Archiving: Data archived at: SRA repository. We used data already available in SRA repository (samples in BioProject PRJNA208335) and also generated new sequence datasets: SRA accession for blood RNA SRR7540238 and GenBank accession number for the assembled mitochondria MH638304.

PY - 2019/1/8

Y1 - 2019/1/8

N2 - BACKGROUND: A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.RESULTS: Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.CONCLUSIONS: Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

AB - BACKGROUND: A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.RESULTS: Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.CONCLUSIONS: Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

KW - international

UR - https://www.ncbi.nlm.nih.gov/bioproject/PRJNA208335

U2 - 10.1186/s12864-018-5378-2

DO - 10.1186/s12864-018-5378-2

M3 - Article

VL - 20

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 19

ER -

ID: 9693997