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A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina.

Authors
  • Friis, Guillermo1
  • Vizueta, Joel2
  • Smith, Edward G1
  • Nelson, David R1
  • Khraiwesh, Basel1, 3
  • Qudeimat, Enas1, 3
  • Salehi-Ashtiani, Kourosh1
  • Ortega, Alejandra4
  • Marshell, Alyssa5
  • Duarte, Carlos M4
  • Burt, John A1
  • 1 Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates. , (United Arab Emirates)
  • 2 Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08007, Spain. , (Spain)
  • 3 Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. , (Saudi Arabia)
  • 4 Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. , (Saudi Arabia)
  • 5 Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman. , (Oman)
Type
Published Article
Journal
G3 Genes|Genome|Genetics
Publisher
The Genetics Society of America
Publication Date
Jan 18, 2021
Volume
11
Issue
1
Identifiers
DOI: 10.1093/g3journal/jkaa025
PMID: 33561229
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4-10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4-1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation. © The Author(s) 2020. Published by Oxford University Press on behalf of Genetics Society of America.

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