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

Guillermo Friis,Alejandra Ortega,John A Burt,Kourosh Salehi-Ashtiani,Edward G Smith,Basel Khraiwesh,David R Nelson,Joel Vizueta,Enas Qudeimat,Carlos M Duarte,Alyssa Marshell,P Ingvarsson

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 (22.4–10.5 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.

Highlights

Mangroves are a polyphyletic group of trees and shrubs that inhabit the intertidal zone of the tropic and subtropic coasts (Nagelkerken et al 2008; Polidoro et al 2010; Hogarth 2015; Primavera et al 2018)
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
Partially allopatric taxa or “varieties” have been described: A. marina var. australasica, restricted to southeastern Australia and New Zealand; A. marina var. eucalyptifolia, in northern regions of Australasia; and A. marina var. marina that ranges from New Caledonia in the Pacific and across the entire Indian Ocean (Duke 1991; Li et al 2016; Tomlinson 2016)

Summary

Introduction

Mangroves are a polyphyletic group of trees and shrubs that inhabit the intertidal zone of the tropic and subtropic coasts (Nagelkerken et al 2008; Polidoro et al 2010; Hogarth 2015; Primavera et al 2018). The diversity of evolutionary origins and adaptive mechanisms found in mangroves provides compelling systems for studying patterns of trait evolution, lineage divergence, and speciation (e.g., Zhou et al 2007; Urashi et al 2013; Xu et al 2017b). We report a high-quality, chromosome-level assembly obtained using proximity ligation libraries as a resource for genome-based studies on A. marina and related mangrove species. We generated whole-genome shotgun data for a set of resequenced individuals from six different populations along the coasts of the Arabian Peninsula. We used these data to evaluate the performance of the assembly as a reference to study patterns of adaptive variability at the genomic level.

Materials and methods

Results and discussion

Literature cited