Sandfish generations: loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Hatcheries are indispensable for seed production of many commercial aquaculture species. However, for mass-spawning species in particular, they can be capricious environments where genetic diversity among progeny may be lost due to small effective broodstock population sizes, variable parental contributions and differential family survival. Understanding the genetic impacts of hatchery production is therefore important for addressing these problems and optimising propagation methods. We used 6051 genome-wide Single Nucleotide Polymorphisms (SNPs) to analyse genetic diversity, parental contributions and offspring kinship during a commercial-scale hatchery production run of sandfish (Holothuria scabra), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were highly skewed, with up to 26% of the parent pool contributing and kinship analyses determined that just two parents sired between 44.4 and 67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD = 1121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13–16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. As many sandfish broodstock remain wild-sourced, maintenance of healthy wild populations as reservoirs of genetic diversity is important, along with selection for spawning of genetically diverse individuals which are as distantly-related as possible

The complete mitochondrial genome of the barcheek trevally, Carangoides plagiotaenia Bleeker, 1857 from Beqa Lagoon in Fiji

The complete mitochondrial genome of the Barcheek trevally, Carangoides plagiotaenia Bleeker, 1857 from Beqa lagoon, Fiji Islands, was determined by high-throughput sequencing (HTS). Its mitogenome (16,551 bp) contained the typical 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 tRNAs, along with two non-coding regions: control region (D-loop) and the origin of light-strand replication (OL). In its mitogenome, one unusual start codon (GTG) was identified in COI and incomplete stop codons (TA-/T–) were predicted in seven PCGs including ND2, COII, ATP6, COIII, ND3, ND4 and CytB. The phylogenetic tree revealed that C. plagiotaenia is sister to C. bajad with 88.75% nucleotide identity in 13 PCGs and 90.49% in the complete mitogenomes

The complete mitochondrial genome of the doubled-lined mackerel Grammatorcynus bilineatus Rüppell, 1836 (Perciformes: Scombridae) from Beqa lagoon in Fiji

The complete mitochondrial genome of the doubled-lined mackerel, Grammatorcynus bilineatus, was determined by the combination of high-throughput sequencing (HTS) and Sanger sequencing. The constructed mitochondrial genome of G. bilineatus was 16,537 bp in length, which harbors a canonical 37 genes (13 proteins, two ribosomal RNAs, and 22 tRNAs) and two non-coding regions (origin of light-strand replication (OL) and the D-loop control region). Among 38 genes, nine were encoded on its light strand (L), while the other 28 were on its heavy strand (H). Besides COX1 (GTG) and ATP6 (CTG), the other eleven protein-coding genes (PCGs) begin with a typical start codon (ATG). The phylogenetic tree showed that G. bilineatus was not clustered with the other species in the Scombridae, forming a clade for Grammatorcynus. The genetic information of G.bilineatus will provide useful information for the scientific management and conservation of the species in the genus