Whole-genome assembly and annotation of little yellow croaker
(Larimichthys polyactis) provide insights into the evolution of
hermaphroditism and gonochorism
The evolutionary direction of gonochorism and hermaphroditism is an
intriguing mystery to be solved. The special transient hermaphroditic
stage makes the little yellow croaker (Larimichthys polyactis, L.
polyactis) an appealing model for studying the formation of
hermaphrodites. On the other hand, as the most famous commercial fish
species in East Asia, the origin and evolutionary relationship of L.
polyactis and Larimichthys crocea remain unclear. Here, we report the
genome sequence of L. polyactis, with a size of ~706 Mb
(contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and 25,233
protein-coding genes. Phylogenomic analysis suggests that L. polyactis
diverged from the common ancestor of Larimichthys crocea
~25.4 million years ago. Our high-quality genome
assembly enabled comparative genomic analysis, which revealed a number
of within-chromosome rearrangements and translocations without major
chromosome fission or fusion events between the two species. The dmrt1
gene was identified as the candidate sex determination gene in L.
polyactis. The expression of dmrt1 and its upstream regulatory gene
rnf183 were both sexually dimorphic in the transcriptome analysis.
Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in
Larimichthys but not in other teleost species, suggesting that it
originated from a lineage-specific duplication or was lost in other
teleosts. Phylogenetic analysis shows that the hermaphrodite stage in
male L. polyactis may be explained by the sequence evolution of dmrt1.
Decoding the L. polyactis genome not only provides insight into the
genetic underpinnings of hermaphrodite evolution but also provides
valuable information for enhancing fish aquaculture.