Current protocols in bioinformatics Chapter 4(Unit 4), 10, https://doi.org/10.1002/0471250953.bi0410s25 (2009). Grobet et al. A total of 20,741 OrthoMCL families were built using the previously all-to-all BLASTP strategy55. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. Divergence times and distribution of different types of orthologues in representative species. & Zhou, Q. Therefore, the TGF-β superfamily has more complex biological functions (Cheifetz et al., 1987; Massague, 1998). Parra, G., Blanco, E. & Guigo, R. GeneID in Drosophila. Bioinformatics 31, 3210–3212, https://doi.org/10.1093/bioinformatics/btv351 (2015). We Using available public datasets of embryo-wide RNA-Seq experiments in zebrafish (https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475) we found that both mstn genes were expressed at the larval stage of protruding mouth, with the highest expression at larval day 4. Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. In olive flounder (Paralichthys olivaceus), CRISPR/Cas9-mediated mstn disruption similarly enhanced muscle mass (Kim et al., 2019). In large yellow croakers, mstn1 was expressed in the liver, kidney, brain, intestine, and skeletal muscle, and mstn2 was expressed in the spleen, brain, adipose, kidney, gill, eye, intestine, and liver (Liu et al., 2014; Xue et al., 2012). Embryos were collected according to developmental stages, including the two-cell stage, blastula stage, gastrula stage, neurula stage, somite appearance stage, eye lens formation stage, muscular activity stage, heart pulsation stage, eye pigment formation stage and hatching stage (Chen, 2005). You can add specific subject areas through your profile settings.
Vertebrate mstns were searched on NCBI genome database (https://www.ncbi.nlm.nih.gov/genome/), followed by analysis online using Splign (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi). Circos plot of the reference genome of T. bimaculatus and syntenic relationship with the T. rubripes genome. First, reads from the short-insert library were re-mapped onto the assembled genome using BWA12 (version 0.7.17). (1997) first discovered it when they studied Belgian blue cattle. These results showed that MSTN could inhibit skeletal muscle growth. De novo identification of repeat families in large genomes. Bioinformatics 22, 2971–2972, https://doi.org/10.1093/bioinformatics/btl505 (2006). Its expression was significantly higher in the eye pigment formation stage and the hatching stage than that in other stages. We removed the reads that did not map within 500 bp of a restriction enzyme site. bimaculatus genome. To verify the accuracy of the contig arrangement in 22 chromosomes, we aligned 7,443 (count) 1 K bp small fragments with 50 K bp spacing as anchors of the assembled genome against the published T. rubripes genome (FUGU5)24,46 to compare consistency between these two genomes. PubMed Thank you for visiting nature.com. Pendleton, M. et al. Computer applications in the biosciences: CABIOS 13, 555–556, https://doi.org/10.1093/bioinformatics/13.5.555 (1997). Draft genome of the Northern snakehead, Channa argus. and H.B. Protein domains were predicted by SMART research tool (http://smart.embl.de/). Therefore, considering that transcriptomic data derived from different tissues will cover distinct sets of expressed genes, it is conceivable that more genes could be validated. Bioinformatics 26, 2460–2461, https://doi.org/10.1093/bioinformatics/btq461 (2010). The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. (14) PASA: version: 2.3.3; parameters: all parameters were set as default.
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