Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala

Abstract

Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.

Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus

“…The size of the final assembled genome was 709.27 Mb, with a GC content of 40.81%, a heterozygosity rate of 1.18%, and a repetitive sequence rate of 35.43%. These values were generally close to the results of the E. muticus genome survey (670 Mb, 41.68%, 1.26%, 35.33%) reported by Song et al [70], but differed significantly from the results of the L. savala genome (790.02 Mb, 39.03%, 0.53%, 40.54%) as determined by Wu et al [23]. The rate of repetitive sequences is a key factor influencing the genome size of species [71].…”

“…The number of chromosomes in the assembled genome of E. muticus was 24, consistent with that of L. savala, T. albacares, and T. maccoyii [23]. The ML tree results indicated that the phylogenetic relationships of these four species were consistent with their morphological classification [72].…”

“…The ML tree results indicated that the phylogenetic relationships of these four species were consistent with their morphological classification [72]. The number of protein-coding genes annotated in the E. muticus genome was 21,949, which was significantly fewer than that in L. savala (23,625), T. albacares (BioProject: PRJEB47267) (24,623), and T. maccoyii (BioProject: PRJEB46021) (24,659). This may be related to their genome sizes (709.27 Mb vs. 790.02 Mb, 792.1 Mb, 782.4 Mb).…”

“…Similarly, there was a significant increase in the expression levels of Atg5 and Lc3 proteins (orthologue of Atg8 protein) in the injury regeneration site of the caudal fin of zebrafish (D. rerio), indicating that atg-mediated autophagy is key for caudal fin regeneration in zebrafish [90]. In the L. savala genome, autophagy-related genes such as atg3, atg4c, and atg12, which are associated with the formation of its elongated whip-like tail, were also detected by positive selection analyses [23]. Meanwhile, the ids, lipa, gla, man2b1, glns, dnase2, and ppt1 genes detected in this study encode various acid hydrolases that function in lysosomes.…”

“…There is also a lack of research to reveal the genetic and evolutionary mechanisms of the species at the genomic level. Although the genome of Lepturacanthus savala, belonging to the family Trichiuridae, and several genes and pathways related to its specific morphological and behavioral characteristics have been established [23], the exact molecular mechanisms associated with these features are not yet clear. Therefore, there is an urgent need to further explore the genomic information of other trichiurids with unique species attributes, such as E. muticus, to gain a comprehensive and in-depth understanding of the molecular mechanisms underlying the formation of this particular taxon of trichiurids.…”