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

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 Mb to 10.5 Mb) accounted for 98 % of the genome assembly,
with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4
Kb to 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.