Evidence-based gene models for structural and functional annotations of the oil palm genome

Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor V Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti

Research output: Contribution to journalArticlepeer-review

90 Downloads (Pure)

Abstract

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data waiting to be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We have annotated 26,059 oil palm genes integrated from two independent gene-prediction pipelines, Fgenesh++ and Seqping. This integrated annotation constitutes a significant improvement in comparison to the preliminary annotation published in 2013. We conducted a comprehensive analysis of intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the high quality of the current genome annotation. 3,658 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further analysis of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstocks, and we identified 42 key genes involved in fatty acid biosynthesis in oil palm. These results provide an important resource for studies of plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.
Original languageEnglish
Article number21
JournalBiology Direct
Volume12:21
DOIs
Publication statusPublished - 8 Sep 2017

Keywords

  • oil palm
  • gene prediction
  • Seqping
  • intronless
  • genes

Fingerprint

Dive into the research topics of 'Evidence-based gene models for structural and functional annotations of the oil palm genome'. Together they form a unique fingerprint.

Cite this