Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation

How plants adapt and diverge in extreme environments is a key question of
plant evolution and ecology. Mangrove invasion of intertidal environments
is facilitated by adaptive phenotypes such as aerial roots, salt-secreting
leaf, and viviparity, and genomic mechanisms including whole genome
duplication and transposable element number reduction. However, a number
of mangroves lack these typical phenotypes. The question we ask is whether
these phenotypically atypical mangroves also have distinct genomic
features? The sibling mangrove species Lumnitzera littorea and Lumnitzera
racemosa provide a model to study this question. We sequenced and
assembled their genomes to chromosome level, together with a closely
related species Combretum micranthum. While most mangroves have small
genomes, the genomes of both Lumnitzera species are large (1443 and 1317
Mb) and carry a high proportion of repeat sequences (~75%). Moreover,
Lumnitzera species have not undergone post-gamma whole-genome
duplications. Their genome size increased mainly due to the expansion of
repeat sequences in their ancestors. However, Lumnitzera genomes have
reduced transposable elements by constraining the proliferation of new
LTR-RTs. Meanwhile, the two species have more gene families contracted
than expanded, and some gene families with reversed size change may
underlie their differentiation in root morphology and local distribution.
We identified 86 chromosomal inversions, five of which are measured
between 6.5 and 12.8 megabases. A number of genes located in these
inversions function in pigment biosynthesis, a process likely involved in
flower color differentiation between the Lumnitzera species. We conclude
that the mangroves with atypical phenotypes also have atypical genomic
evolution.