Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae

Author:

Low Eng-Ti Leslie1ORCID,Chan Kuang-Lim1ORCID,Zaki Noorhariza Mohd1,Taranenko Elizaveta2,Ordway Jared M3ORCID,Wischmeyer Corey3,Buntjer Jaap3,Halim Mohd Amin Ab1,Sanusi Nik Shazana Nik Mohd1,Nagappan Jayanthi1,Rosli Rozana1,Bondar Eugeniya2,Amiruddin Nadzirah1,Sarpan Norashikin1,Ting Ngoot-Chin1,Chan Pek-Lan1,Ong-Abdullah Meilina1,Marjuni Marhalil1,Mustaffa Suzana1,Abdullah Norziha1,Azizi Norazah1,Bacher Blaire3,Lakey Nathan3,Tatarinova Tatiana V2ORCID,Manaf Mohamad Arif Abd1,Sambanthamurti Ravigadevi1,Singh Rajinder1

Affiliation:

1. Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board , 6 Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor , Malaysia

2. Biology Department, University of La Verne , La Verne, CA 91750 , USA

3. Orion Genomics , 3730 Foundry Way, St. Louis, MO 63110 , USA

Abstract

Abstract Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.

Funder

11th Malaysia Plan

Rancangan Malaysia Ke-11

Publisher

Oxford University Press (OUP)

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