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Sequencing and Assembly of the Pineapple Genome

  • Jishan Lin
  • Ray MingEmail author
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)

Abstract

Pineapple (Ananas comosus L.) is an important tropical fruit crop, not only because of its economic value but also due to its CAM photosynthesis that exhibits the highest water-use efficiency comparing to plants with C3 and C4 photosynthesis. The genome of pineapple variety F153 was sequenced using a combination of DNA sequencing technologies, including Illumina, Moleculo, 454, and PacBio single-molecule long reads. Pooled bacterial artificial chromosome (BAC) sequences were used to assist the genome assembly, and the final assembly reached 382 Mb, 72.6% of the estimated 526 Mb. An ultrahigh-density genetic map with 25 linkage groups was used to correct chimeric scaffolds and anchored 564 scaffolds, covering 316 Mb, or 82.7%, of the assembled genome. The pineapple genome was annotated by MAKER and 27,024 genes, and 10,151 alternative splicing events were identified. Transposable elements (TEs) accounted for 44% of the assembly. The 27.4% unassembled sequences are all highly repetitive centromere, telomere, and rDNA clusters (2.4%) and TEs (25%), indicating that TEs accounted for 69% of the pineapple genome. LTR retrotransposons were the most abundant of TEs, representing 33% of the assembly. Intragenomic syntenic analysis of pineapple genome traced karyotype evolution from seven monocot ancestral chromosomes to current 25 chromosomes, and two ancient whole-genome duplication (WGD) events (σ and τ) in pineapple genome were detected, but not the more recent ρ WGD. Candidate genes involved in the carbon fixation module of CAM were identified in the pineapple genome, and nine genes were found to have a diurnal expression pattern in the green leaf tissue. CAM-related genes were enriched with circadian clock cis-regulatory elements. The pineapple genome will accelerate the progress relevant to fundamental biology and/or pineapple production, including drought tolerance.

Keywords

Ananas comosus Cis-element Genome sequencing Karyotype Whole-genome duplication 

Notes

Acknowledgment

We thank Duane Bartholomew for providing the historic information of Smooth Cayenne clone Champaka F153.

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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