Tag: MCScanX
Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales
Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…
Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes
Reconstruction of gene and macro-synteny trees for the three studied Papaver species Syntenic blocks within the three Papaver species were identified with OrthoFinder v2.3.15. Orthologous and paralogous relationships, as well as orthogroups, were inferred using the parameters “-M msa -T fasttree” based on proteome sequences from multiple species. The resulting…
Input file for Synteny visualization with SynVisio
Input file for Synteny visualization with SynVisio 0 I am trying to visualize synteny relationship by using SynVisio tool. but I am not able to understand the input file format Collinearity file. I am providing MCScanX Output, but the software is not accepting it. kindly help me with input collinearity…
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article Google Scholar Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…
Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis
Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article CAS PubMed Google Scholar Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm
Gupta, A., Rico-Medina, A. & Cano-Delgado, A. I. The physiology of plant responses to drought. Science 368, 266–269 (2020). Article CAS PubMed Google Scholar Hu, H. & Xiong, L. Genetic engineering and breeding of drought-resistant crops. Annu Rev. Plant Biol. 65, 715–741 (2014). Article CAS PubMed Google Scholar Ashraf, M….
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Global peatland dynamics since the Last Glacial Maximum. Geophys. Res. Lett. 37, L13402 (2010). van Breemen, N. How Sphagnum bogs down other plants. Trends Ecol. Evol. 10, 270–275 (1995). Article Google Scholar Johnson, M. G. et…
Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes
Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article Google Scholar Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…
MCScanX file types – ECHEMI
30 Upvotes · 4 Comments 30 Upvotes · 3 Comments 29 Upvotes · 1 Comments 28 Upvotes · 3 Comments 27 Upvotes · 2 Comments 26 Upvotes · 2 Comments 24 Upvotes · 1 Comments Read more here: Source link
help for old version of MCScanX for parameter U
Dr Wang: In the early vserions of MSCanX, the parameter “u” designated the intergenetic distance (defualt value:10kb). This may be true for angiosperms, but recently, we sequenced a fern genome, and found the average genetic distance about 100kb, We have used the updated version of MCSCanX, the propotions of synteny…
MCScanX: not found – githubmate
Hi CJ-Chen, Thanks for developing this tool. I having an issue when I try to use Quick Run MCScanX Wrapper. error log here: [Debug…All Standard Error Info will show as following:…] Curr log file:/tmp/TBtools.14595798488989250861.20210723103734.log Curr java version:11.0.11 Curr TBtools version:1.09854 Maxmum Memory for Curr TBtools: 4162846720 curVersion:1.09854:force Fetch Location:200 Factor:0.1516546094367225…
Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)
1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed Google Scholar 2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS PubMed PubMed Central Google Scholar 3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…
MCScanX empty collinearity file.
MCScanX empty collinearity file. 1 Hellow, I want to check the gene duplication of a gene within Potato genome for which I am using MCScanX. ./MCScanX data/xyz OUTPUT is showing that there is no alingment generated: Reading BLAST file and pre-processing Generating BLAST list 1446 matches imported (1155 discarded) 48…
