Ecological adaptation of Atlantic Herring (Clupea harengus) in the Baltic Sea
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PROVIDER: PRJEB32358 | ENA |
REPOSITORIES: ENA
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Project description:Strong signatures of selection in Atlantic herring: A marine fish with huge population sizes
| PRJNA179109 | ENA
Project description:Strong signatures of selection in Atlantic herring: A marine fish with huge population sizes
| PRJNA179110 | ENA
Project description:Comparison of herring populations across the North Atlantic Ocean
| PRJNA338612 | ENA
Project description:The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.
| S-EPMC3413699 | biostudies-literature
Project description:Baltic herring (Clupea harengus membras) is a total spawner with a group-synchronous ovarian organization. Age polymodality in total spawners is considered an important factor in assuring that a strong population is sustainable under an intensive harvesting regime and different climatic conditions. In the present study, we investigated the seasonal and inter-annual variation in spawner age structure and the effect of preceding winter thermal conditions on the start of the herring spawning and larvae retention period. Herring spawning season in the Gulf of Riga starts up to six weeks later after colder winters compared to milder winters. Significantly older individuals dominated at the beginning of the spawning season, and thus herring mean age gradually decreased towards the end of the spawning season from 1999-2015. On an annual scale, this pattern was obvious after cold winters, while after mild winters the pattern did not continue, indicating a more homogenous maturation cycle and spawning period, despite the age and size of the herring population in mild winters. Further, herring condition factor was studied in relation to age and spawning season following different winter thermal conditions. Young, 2- and 3- year old first-spawning herring experienced significantly lower conditions after cold winters compared to older ages, indicating an age-dependent effect of preceding winter on herring maturation cycle, condition and spawning time.
| S-EPMC6657675 | biostudies-literature
Project description:Because of the high management relevance, commercial fish related aspects have often been central in marine ecosystem investigations. The iterative shiftogram method was applied to detect occurrence, type and timing of shifts in the single and multivariate time series linked to the spring spawning herring larvae in the Gulf of Riga (Baltic Sea). Altogether nineteen larval herring and related environmental variables were utilized during the period of 1957-2010. All the time series investigated, either single or multivariate, exhibited one or more shifts with variable type and timing. Multivariate shiftogram based on all time series identified two distinct states (1957-1983 and 1992-2010) in studied variables, separated by a smooth transition period lasting almost ten years. The observed shift was mainly related to hydroclimate and not to phenology or biota. Significantly increased variability was found in larval herring and recruitment abundances after the shift. While the shift in hydroclimate (1985-1991) was followed by the shift in phenology (1991-1997), the shift in biota occurred remarkably later (2003). It is likely that the dynamics in biota were affected by other drivers than those investigated in the current paper.
| S-EPMC3956613 | biostudies-literature
Project description:Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.
| S-EPMC6881392 | biostudies-literature
Project description:The sex determination system of Atlantic herring Clupea harengus L., a commercially important fish, was investigated. Low coverage whole-genome sequencing of 48 females and 55 males and a genome-wide association study revealed two regions on chromosomes 8 and 21 associated with sex. The genotyping data of the single nucleotide polymorphisms associated with sex showed that 99.4% of the available female genotypes were homozygous, whereas 68.6% of the available male genotypes were heterozygous. This is close to the theoretical expectation of homo/heterozygous distribution at low sequencing coverage when the males are factually heterozygous. This suggested a male heterogametic sex determination system in C. harengus, consistent with other species within the Clupeiformes group. There were 76 protein coding genes on the sex regions but none of these genes were previously reported master sex regulation genes, or obviously related to sex determination. However, many of these genes are expressed in testis or ovary in other species, but the exact genes controlling sex determination in C. harengus could not be identified.
| S-EPMC7115899 | biostudies-literature
Project description:Identification and characterization of coding and noncoding TSHR polymorphisms affecting photoperiodic regulation of reproduction in Atlantic herring
| PRJNA660525 | ENA