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

Citation

Friis, G and Vizueta, J and Smith, EG and Nelson, DR and Khraiwesh, B and Qudeimat, E and Salehi-Ashtiani, K and Ortega, A and Marshell, A and Duarte, CM and Burt, JA, A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina, Genes, Genomes, Genetics, 11, (1) Article jkaa025. ISSN 2160-1836 (2020) [Refereed Article]


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Copyright Statement

Copyright The Author(s) 2020. Published by Oxford University Press on behalf of Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

DOI: doi:10.1093/g3journal/jkaa025

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 (22.410.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.41 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.

Item Details

Item Type:Refereed Article
Keywords:gray mangrove, Avicennia marina, genome assembly, HiC, Arabia
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Marine and estuarine ecology (incl. marine ichthyology)
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Assessment and management of benthic marine ecosystems
UTAS Author:Marshell, A (Dr Alyssa Marshell)
ID Code:148946
Year Published:2020
Web of Science® Times Cited:6
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2022-02-24
Last Modified:2022-04-26
Downloads:3 View Download Statistics

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