PacBio sequencing of gene families - A case study with wheat gluten genes

Wei Zhang, Paul Ciclitira, Joachim Messing*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)

Abstract

Amino acids in wheat (Triticum aestivum) seeds mainly accumulate in storage proteins called gliadins and glutenins. Gliadins contain alpha/beta-, gamma- and omega-types whereas glutenins contain HMW- and LMW-types. Known gliadin and glutenin sequences were largely determined through cloning and sequencing by capillary electrophoresis. This time-consuming process prevents us to intensively study the variation of each orthologous gene copy among cultivars. The throughput and sequencing length of Pacific Bioscience RS (PacBio) single molecule sequencing platform make it feasible to construct contiguous and non-chimeric RNA sequences. We assembled 424 wheat storage protein transcripts from ten wheat cultivars by using just one single-molecule-real-time cell. The protein genes from wheat cultivar Chinese Spring are comparable to known sequences from NCBI. We demonstrated real-time sequencing of gene families with high-throughput and low-cost. This method can be applied to studies of gene amplification and copy number variation among species and cultivars. 

Original languageEnglish
Article numberN/A
Pages (from-to)541-546
Number of pages6
JournalGene
Volume533
Issue number2
DOIs
Publication statusPublished - 10 Jan 2014

Keywords

  • PacBio sequencing
  • Gene family
  • Gluten diversity
  • Copy number variation
  • Repetitive sequence
  • MAIZE
  • ZEIN
  • DNA

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