PacBio for haplotyping in gene families

Wei Zhang, Joachim Messing

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing. Sequencing reads were later separated by the barcodes and further sorted into different gene groups by blast. The reads from each gene are then assembled by SeqmanNGen software. Given the length of 1 kb for each sequence derived from an initial molecule, the phase of the polymorphisms is not lost and can be used to infer also haplotype differences between different cultivars.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages61-71
Number of pages11
DOIs
StatePublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
Volume1551

Fingerprint

Genes
Glutens
Nucleic Acid Repetitive Sequences
Haplotypes
Libraries
Triticum
Software

All Science Journal Classification (ASJC) codes

  • Genetics
  • Molecular Biology

Cite this

Zhang, W., & Messing, J. (2017). PacBio for haplotyping in gene families. In Methods in Molecular Biology (pp. 61-71). (Methods in Molecular Biology; Vol. 1551). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6750-6_3
Zhang, Wei ; Messing, Joachim. / PacBio for haplotyping in gene families. Methods in Molecular Biology. Humana Press Inc., 2017. pp. 61-71 (Methods in Molecular Biology).
@inbook{2fa9b526f01544c3b5b4adff27b84739,
title = "PacBio for haplotyping in gene families",
abstract = "The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing. Sequencing reads were later separated by the barcodes and further sorted into different gene groups by blast. The reads from each gene are then assembled by SeqmanNGen software. Given the length of 1 kb for each sequence derived from an initial molecule, the phase of the polymorphisms is not lost and can be used to infer also haplotype differences between different cultivars.",
author = "Wei Zhang and Joachim Messing",
year = "2017",
month = "1",
day = "1",
doi = "https://doi.org/10.1007/978-1-4939-6750-6_3",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "61--71",
booktitle = "Methods in Molecular Biology",

}

Zhang, W & Messing, J 2017, PacBio for haplotyping in gene families. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1551, Humana Press Inc., pp. 61-71. https://doi.org/10.1007/978-1-4939-6750-6_3

PacBio for haplotyping in gene families. / Zhang, Wei; Messing, Joachim.

Methods in Molecular Biology. Humana Press Inc., 2017. p. 61-71 (Methods in Molecular Biology; Vol. 1551).

Research output: Chapter in Book/Report/Conference proceedingChapter

TY - CHAP

T1 - PacBio for haplotyping in gene families

AU - Zhang, Wei

AU - Messing, Joachim

PY - 2017/1/1

Y1 - 2017/1/1

N2 - The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing. Sequencing reads were later separated by the barcodes and further sorted into different gene groups by blast. The reads from each gene are then assembled by SeqmanNGen software. Given the length of 1 kb for each sequence derived from an initial molecule, the phase of the polymorphisms is not lost and can be used to infer also haplotype differences between different cultivars.

AB - The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing. Sequencing reads were later separated by the barcodes and further sorted into different gene groups by blast. The reads from each gene are then assembled by SeqmanNGen software. Given the length of 1 kb for each sequence derived from an initial molecule, the phase of the polymorphisms is not lost and can be used to infer also haplotype differences between different cultivars.

UR - http://www.scopus.com/inward/record.url?scp=85011371588&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85011371588&partnerID=8YFLogxK

U2 - https://doi.org/10.1007/978-1-4939-6750-6_3

DO - https://doi.org/10.1007/978-1-4939-6750-6_3

M3 - Chapter

T3 - Methods in Molecular Biology

SP - 61

EP - 71

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

Zhang W, Messing J. PacBio for haplotyping in gene families. In Methods in Molecular Biology. Humana Press Inc. 2017. p. 61-71. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-6750-6_3