Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish.

Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexual reproduction has been maintained for over 0.82 million years. Comparative genomics show intensive expansion and alterations of meiotic cell cycle-related genes and an oocyte-specific histone variant. Cytological assays indicate that C. gibelio produces unreduced oocytes by an alternative ameiotic pathway; however, sporadic homologous recombination and a high rate of gene conversion also exist in C. gibelio. These genomic changes might have facilitated purging deleterious mutations and maintaining genome stability in this unisexual amphitriploid fish. Overall, the current results provide novel insights into the evolutionary mechanisms of the reproductive success in unisexual polyploid vertebrates.

Author Correction: Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

In the original version of this Data Descriptor the word "Gulf" was incorrectly spelled in the affiliation "Ocean College, Beibu Gulf University, Qinzhou, 535011, Guangxi, China". This has now been corrected in both the HTML and PDF versions.

Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus.

Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.

MOTIVATION: Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files. RESULTS: We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported. AVAILABILITY AND IMPLEMENTATION: PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.

[Experimental research of therapeutic effect on hepatocellular carcinoma of targeting SMYD3 gene inhibition by RNA interference].

OBJECTIVE: To determine the potential of SMYD3 as a therapeutic target for hepatocellular carcinoma (HCC) by potent and highly sequence-specific RNA interference (RNAi) technique. METHODS: The mRNA of SMYD3 was detected by RT-PCR in different HCC cell lines, such as HepG2, Hep3B and SMMC7721. Recombinant SMYD3 shRNA plasmid Pgenesil-1-s was constructed and transfected into HepG2 cells, and Western blot was used to identify the down regulation of SMYD3 protein expression after transfection. MTT and flow cytometry analysis (FCM) were respectively applied to analysis cell proliferation and apoptosis. In vivo study was carried out by injecting recombinant SMYD3 shRNA plasmids into transplanted tumors of nude mice. RESULTS: The expression of SMYD3 mRNA was abundant in HCC cell lines HepG2, Hep3B, SMMC7721, whereas none in normal hepatic cell line L-02. RNA interference was able to suppress SMYD3 expression greatly and then inhibited cell growth effectively and induced apoptosis of HepG2 cells efficiently. After injection of recombinant SMYD3 shRNA plasmid, transplanted tumors grew slowly and reduced in size and weight when compared with those of control groups (P < 0.01). CONCLUSIONS: SMYD3 plays a major role in occurrence and progress of HCC. Inhibition of SMYD3 by RNAi can induce apoptosis in HepG2 cells and suppress tumor growth in nude mice. Therefore SMYD3 could be an ideal therapeutic target for HCC.

[Inhibition of SMYD3 gene expression by RNA interference induces apoptosis in human hepatocellular carcinoma cell line HepG2].

BACKGROUND & OBJECTIVE: SET and MYND domain-containing protein 3 (SMYD3) gene was found to encode a histone methyltransferase involved in the proliferation and apoptosis of cancer cells. This study was to detect the expression of SMYD3 in hepatocellular carcinoma (HCC) cell lines, and reveal its function of regulating proliferation and apoptosis of HCC cell line through gene silencing. METHODS: The expression of SMYD3 in HCC cell lines HepG2, Hep3B, SMMC7721, and normal hepatic cell line L-02 was detected by reverse transcription-polymerase chain reaction (RT-PCR); its expression in 24 specimens of HCC and peri-cancer tissue was detected by immunohistochemistry. Short hairpin RNA (shRNA) plasmids Pgenesil-1-s1 and Pgenesil-1-s2 (with interfering effect), and Pgenesil-1-hk (without interfering effect) were constructed and transfected into HepG2 cells. Western blot was used to detect the expression of SMYD3 protein after transfection. Cell proliferation was analyzed by MTT assay; cell apoptosis was analyzed by flow cytometry (FCM) and TUNEL. RESULTS: SMYD3 was overexpressed in the HCC cell lines and HCC tissue. After transfection with shRNA, SMYD3 expression in HepG2 cells was down-regulated by 75%-85%, and the cell growth was inhibited by 60.95%-72.14%. The apoptosis rate of HepG2 cells was significantly higher in Pgenesil-1-s1 and Pgenesil-1-s2 groups than in Pgenesil-1-hk and Pgenesil-1 groups [(17.68+/-2.36)% and (19.07+/-1.78)%, vs. (1.44+/-0.28)% and (0.47+/-0.12)%, P<0.01]. CONCLUSION: SMYD3 is overexpressed in various HCC cell lines and HCC tissue; RNA interference can down-regulate SMYD3 expression, inhibit proliferation and promote apoptosis of HepG2 cells.

[Suppression of SMYD3 expression in HepG2 cell by shRNA interference].

OBJECTIVES: To identify the inhibition effect of shRNA on the SMYD3 (SET- and MYND-domain containing protein-3) expression in hepatoma cell line HepG2 through gene silencing. METHODS: Two reverse repeated motifs targeting on the SMYD3 mRNA sequences 267-288, 302-323 respectively, were synthesized and inserted into the mock plasmid pGenesil-1 which expressed EGFP to create recombinant plasmids pGenesil-1-s1 and pGenesil-1-s2. pGenesil-1-hk specific to no SMYD3 mRNA sequence served as a control. After transfection into HepG2 cells, RT-PCR and western blot were applied to identify the down regulation of SMYD3 expression by shRNAs. RESULTS: All plasmids were constructed successfully. pGenesil-1-s1, pGenesil-1-s2 inhibited the mRNA and protein expression of SMYD3 in HepG2 cells. There was a significant distinction when compared with pGenesil-1-hk and pGenesil-1 (P<0.01). CONCLUSION: Short hairpin RNAs can efficiently and specifically suppress the expression of SMYD3 in HepG2 cells.