Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis

Fertilization capacity with rainbow trout DNA-damaged sperm and embryo developmental success

Mammalian spermatozoa undergo a strong selection process along the female tract to guarantee fertilization by good quality cells, but risks of fertilization with DNA-damaged spermatozoa have been reported. In contrast, most external fertilizers such as fish seem to have weaker selection procedures. This fact, together with their high prolificacy and external embryo development, indicates that fish could be useful for the study of the effects of sperm DNA damage on embryo development. We cryopreserved sperm from rainbow trout using egg yolk and low-density lipoprotein as additives to promote different rates of DNA damage. DNA fragmentation and oxidization were analyzed using comet assay with and without digestion with restriction enzymes, and fertilization trials were performed. Some embryo batches were treated with 3-aminobenzamide (3AB) to inhibit DNA repair by the poly (ADP-ribose) polymerase, which is an enzyme of the base excision repair pathway. Results showed that all the spermatozoa cryopreserved with egg yolk carried more than 10% fragmented DNA, maintaining fertilization rates of 61.1+/-2.3 but a high rate of abortions, especially during gastrulation, and only 14.5+/-4.4 hatching success. Furthermore, after 3AB treatment, hatching dropped to 3.2+/-2.2, showing that at least 10% DNA fragmentation was repaired. We conclude that trout sperm maintains its ability to fertilize in spite of having DNA damage, but that embryo survival is affected. Damage is partially repaired by the oocyte during the first cleavage. Important advantages of using rainbow trout for the study of processes related to DNA damage and repair during development have been reported. Reproduction (2010) 139 989-997Junta de Castilla y Leon (Spain) [LE007A06]; University of Leoninfo:eu-repo/semantics/publishedVersio

Effects of the slow cooling during cryopreservation on the survival and morphology of Taiwan shoveljaw carp (Varicorhinus barbatulus) spermatozoa

Over the past decades, pollution, overfishing, and habitat degradation have driven the population size of Taiwan shoveljaw carp down markedly in Taiwan. Cryopreservation is a useful tool which could be used to maintain genetic resources to protect and preserve this endemic species. Four cryoprotectants [dimethyl sulphoxide (DMSO), dimethylacetamide (DMA), glycerol and methanol] and six freezing rates (0.5, 1, 2, 4, 8, 16 °C min-1) were tested in order to develop an optimal controlled slow-freezing protocol for Taiwan shoveljaw carp spermatozoa. Samples were subsequently examined under the scanning electron microscope to reveal whether cryopreservation had affected their ultrastructural morphology. The highest survival rate (50.1 ± 2.0%) was observed with a freezing rate of 8 °C min-1 in 1M DMSO, using SYBR-14 + PI staining. Fertility and hatching rate results using frozen-thawed spermatozoa (90.2 ± 2.2% and 22.3 ± 2.5%, respectively) were not significantly different from results with fresh spermatozoa. After cryopreservation, 21.0 ± 1.6% of frozen-thawed spermatozoa had mid-piece swelling and rupture of the head. Cryopreservation might, therefore, slightly affect Taiwan shoveljaw carp spermatozoa in terms of morphological change. However, these alterations could be compensated by using large enough numbers of normally functioning frozen-thawed spermatozoa to achieve a standard equal to fresh spermatozoa. This is the first report of successful cryopreservation of Taiwan shoveljaw carp spermatozoa using a controlled slow-cooling method

Induced triploidy in the common carp

Cold shocks and hydrostatic pressure shocks, respectively, were applied for the induction of both triploidy and tetraploidy in the common carp. Cold shocks of 0-2 °C, lasting 40 minutes and starting 2–5 minutes after the activation of gametes and hydrostatic pressure shocks with 1-3-5 minute exposures at 49.03–56.88 MPa (i. e. 7 116-8 225 psi – pounds per square inch), starting 5 minutes after the activation of gametes gave the best results. The tetraploidy induction by cold shocks or hydrostatic pressure shocks resulted either in negligible (1.54%), or in zero yields, respectively. The applicability of particular types of ploidy manipulation and the standardization of shock initiation were discussed

Genetic variability and differentiation of wild and cultured tench populations inferred from microsatellite loci

Nine species-specific microsatellites were used to characterize 792 tench, Tinca tinca (L.), from 21 wild and cultured populations. Seven loci were polymorphic expressing four to 22 alleles. A Spanish cultured strain was homozygous at all loci for all individuals studied. Low variability was also observed in a wild population from Sapanca Lake, Turkey and a Chinese cultured strain. In contrast, the highest variabilities were found in wild tench from lake Felchowsee (average number of alleles), and the cultured strain from Konigswartha (average heterozygosity), both from Germany. Genetic differentiation between populations was moderate to high. The smallest genetic distances were found between the geographically most distant populations. A Neighbor-Joining tree showed only two major clades consisting of 4 and 17 populations, respectively. Within the smaller clade the Turkish wild and Spanish and Chinese cultured tench formed a sub-cluster with 100% bootstrap support. Possible reasons for the latter unexpected grouping are discussed