The Geminiviridae family is a group of single-stranded DNA viruses that cause important economic losses worldwide (Hanley-Bowdoin et al., 1999; Rojas et al., 2005). Nine genera (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus, Turncurtovirus, Capulavirus and Grablovirus) are currently recognized based upon the type of insect vector, host range, genome organization and phylogeny (Brown et al., 2012; Varsani et al., 2014,Varsani et al., 2017). All have monopartite genomes, with the exception of viruses classified in the genus Begomovirus, which can be monopartite (a single genomic DNA of approx. 2.9 kb) or bipartite (two genomic DNA components of approx. 2.6 kb, referred to as DNA-A and DNA-B) (Brown et al., 2012) (Figure 1).
Figure 1. Genomic organization of the seven genera in the family Geminiviridae. LIR, long intergenic region; SIR, short intergenic region; CR, common region; CP, capsid protein; Rep, replication-associated protein; TrAP, transactivator protein; REn, replication enhancer; MP, movement protein; NSP, nuclear shuttle protein; Reg, regulatory gene; SD, symptom determinant; SS, silencing suppressor; TGS, transcriptional gene silencing. Note that the DNA-A component of Old World bipartite geminiviruses contains a V2 ORF (adapted from Varsani et al., 2017).
The association of geminiviruses with two types of ssDNA satellites (alpha- and betasatellites) has been well documented (Zhou, 2013). These molecules are half the size of viral genome components (approximately 1.35 kb), many of them modulate the symptoms caused by the helper geminiviruses, and are dependent on them for their replication (only in the case of betasatellites), encapsidation and vector transmission (Briddon et al., 2003; Briddon & Stanley, 2006).
Alphasatellites are similar to the DNA-R component of nanoviruses, containing a single ORF, which encodes a replication-associated protein (Rep). They have an A-rich region and a predicted stem-loop structure. The A-rich region is the only feature that can be used to distinguish alphasatellites from nanovirus DNA-R components and it has been suggested that this region may function to increase the size of alphasatellite molecules to half the size of begomovirus genomic components. The predicted alphasatellite stem-loop structure has a loop containing a nonanucleotide, TAGTATTAC, common to nanoviruses that is also similar to the TAATATTAC nonanucleotide sequence in geminiviruses. Alphasatellites are typically associated with monopartite geminiviruses from the Old World that are also associated with betasatellites. Only recently have alphasatellites been found associated to New World bipartite geminiviruses (Paprotka et al., 2010; Romay et al., 2010). These satellites do not significantly contribute to disease development. They can replicate autonomously, but require the helper virus for systemic infection and insect transmission (Briddon & Stanley, 2006).
Betasatellites contain a single ORF, which encodes a pathogenicity determinant protein known as betaC1. These agents contribute for the development of typical disease symptoms, enhance pathogenicity of their helper geminiviruses pathogenicity, and modulate virus host range by modulation of host defense response (Saunders et al., 2004; Saeed et al., 2005). Betasatellite genomes share no significant sequence homology with their helper geminiviruses other than a potential stem-loop structure containing the TAATATTAC sequence. Nevertheless, they have a highly conserved genome organization consisting of a region known as the satellite conserved region (SCR), the betaC1 ORF (conserved both in sequence and position among betasatellites) and an adenine-rich region.
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R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/.
blastp: 2.2.29+ Package: blast 2.2.29, build Jul 1 2014 18:29:55
blastn: 2.2.29+ Package: blast 2.2.29, build Jul 1 2014 18:29:55
CLUSTAL 2.1 Multiple Sequence Alignments DATA (sequences) -INFILE=file.ext :input sequences. -PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment). VERBS (do things) -OPTIONS :list the command line parameters -HELP or -CHECK :outline the command line params. -FULLHELP :output full help content. -ALIGN :do full multiple alignment. -TREE :calculate NJ tree. -PIM :output percent identity matrix (while calculating the tree) -BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000). -CONVERT :output the input sequences in a different file format. PARAMETERS (set things) ***General settings:**** -INTERACTIVE :read command line, then enter normal interactive menus -QUICKTREE :use FAST algorithm for the alignment guide tree -TYPE= :PROTEIN or DNA sequences -NEGATIVE :protein alignment with negative values in matrix -OUTFILE= :sequence alignment file name -OUTPUT= :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA -OUTORDER= :INPUT or ALIGNED -CASE :LOWER or UPPER (for GDE output only) -SEQNOS= :OFF or ON (for Clustal output only) -SEQNO_RANGE=:OFF or ON (NEW: for all output formats) -RANGE=m,n :sequence range to write starting m to m+n -MAXSEQLEN=n :maximum allowed input sequence length -QUIET :Reduce console output to minimum -STATS= :Log some alignents statistics to file ***Fast Pairwise Alignments:*** -KTUPLE=n :word size -TOPDIAGS=n :number of best diags. -WINDOW=n :window around best diags. -PAIRGAP=n :gap penalty -SCORE :PERCENT or ABSOLUTE ***Slow Pairwise Alignments:*** -PWMATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename -PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename -PWGAPOPEN=f :gap opening penalty -PWGAPEXT=f :gap opening penalty ***Multiple Alignments:*** -NEWTREE= :file for new guide tree -USETREE= :file for old guide tree -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename -DNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename -GAPOPEN=f :gap opening penalty -GAPEXT=f :gap extension penalty -ENDGAPS :no end gap separation pen. -GAPDIST=n :gap separation pen. range -NOPGAP :residue-specific gaps off -NOHGAP :hydrophilic gaps off -HGAPRESIDUES= :list hydrophilic res. -MAXDIV=n :% ident. for delay -TYPE= :PROTEIN or DNA -TRANSWEIGHT=f :transitions weighting -ITERATION= :NONE or TREE or ALIGNMENT -NUMITER=n :maximum number of iterations to perform -NOWEIGHTS :disable sequence weighting ***Profile Alignments:*** -PROFILE :Merge two alignments by profile alignment -NEWTREE1= :file for new guide tree for profile1 -NEWTREE2= :file for new guide tree for profile2 -USETREE1= :file for old guide tree for profile1 -USETREE2= :file for old guide tree for profile2 ***Sequence to Profile Alignments:*** -SEQUENCES :Sequentially add profile2 sequences to profile1 alignment -NEWTREE= :file for new guide tree -USETREE= :file for old guide tree ***Structure Alignments:*** -NOSECSTR1 :do not use secondary structure-gap penalty mask for profile 1 -NOSECSTR2 :do not use secondary structure-gap penalty mask for profile 2 -SECSTROUT=STRUCTURE or MASK or BOTH or NONE :output in alignment file -HELIXGAP=n :gap penalty for helix core residues -STRANDGAP=n :gap penalty for strand core residues -LOOPGAP=n :gap penalty for loop regions -TERMINALGAP=n :gap penalty for structure termini -HELIXENDIN=n :number of residues inside helix to be treated as terminal -HELIXENDOUT=n :number of residues outside helix to be treated as terminal -STRANDENDIN=n :number of residues inside strand to be treated as terminal -STRANDENDOUT=n:number of residues outside strand to be treated as terminal ***Trees:*** -OUTPUTTREE=nj OR phylip OR dist OR nexus -SEED=n :seed number for bootstraps. -KIMURA :use Kimura's correction. -TOSSGAPS :ignore positions with gaps. -BOOTLABELS=node OR branch :position of bootstrap values in tree display -CLUSTERING= :NJ or UPGMA
/usr/bin/mafft: Cannot open -h. ------------------------------------------------------------------------------ MAFFT v7.205 (2014/10/20) http://mafft.cbrc.jp/alignment/software/ MBE 30:772-780 (2013), NAR 30:3059-3066 (2002) ------------------------------------------------------------------------------ High speed: % mafft in > out % mafft --retree 1 in > out (fast) High accuracy (for <~200 sequences x <~2,000 aa/nt): % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) If unsure which option to use: % mafft --auto in > out --op # : Gap opening penalty, default: 1.53 --ep # : Offset (works like gap extension penalty), default: 0.0 --maxiterate # : Maximum number of iterative refinement, default: 0 --clustalout : Output: clustal format, default: fasta --reorder : Outorder: aligned, default: input order --quiet : Do not report progress --thread # : Number of threads (if unsure, --thread -1)
Invalid command line option "help" MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. Basic usage muscle -in
-out Common options (for a complete list please see the User Guide): -in Input file in FASTA format (default stdin) -out Output alignment in FASTA format (default stdout) -diags Find diagonals (faster for similar sequences) -maxiters Maximum number of iterations (integer, default 16) -maxhours Maximum time to iterate in hours (default no limit) -html Write output in HTML format (default FASTA) -msf Write output in GCG MSF format (default FASTA) -clw Write output in CLUSTALW format (default FASTA) -clwstrict As -clw, with 'CLUSTAL W (1.81)' header -log[a] Log to file (append if -loga, overwrite if -log) -quiet Do not write progress messages to stderr -version Display version information and exit Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2 Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3 Fastest possible (nucleotides): -maxiters 1 -diags