Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna

Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing

Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai of Anhui province, where rodents are projected to be the main reservoir. This may lead to a critical need of molecular tools with high efficiency in monitoring the dynamic of the rodent-associated S. japonicum, as an appropriate amount of schistosome input can re-establish its life cycle in a place with snails and then result in the re-emergence of schistosomiasis. Therefore, the goal of this study was to develop high polymorphic microsatellites from the whole genome of rodent-associated S. japonicum strain to monitor its transmission dynamic. We sampled the hilly schistosome isolate from Shitai of Anhui in China and sequenced the parasite with the next-generation sequencing technology. The whole genome was assembled with four different approaches. We then developed 71 microsatellite markers at a genome-wide scale throughout two best assembled genomes. Based on their chromosome mapping and the expected length of targeted sequences, we selected 24 markers for the development of multiplex reactions. Two multiplexes composed of 10 loci were finally developed, and their potential was revealed by their successful application on and capturing the genetic diversity of three schistosome populations. The selected 10 markers, each with clear chromosome location and characteristics, will be greatly useful in tracing the dispersal pathways or/and dynamics of the rodent-associated S. japonicum or others in the hilly area of China or elsewhere.

Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing

Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology

Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species’ biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species’ dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length–weight relationship only showed significant male–female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.