MUSTANG is a novel family of domesticated transposase genes ...
MUSTANG is a novel family of domesticated transposase genes ... MUSTANG is a novel family of domesticated transposase genes ...
Figure 1 Relationships between monocot and dicot mudrA genes as determined by clustering at 40% identity. The number of clusters of various sizes is shown for monocot (diagonal fill), dicot (light grey fill) and ‘other’ (dark grey fill). The number of MUG (M) and FAR1 (F) clusters of a given size is indicated by a number or is equal to one where labeled with no number. The ‘Number of Clusters’ axis is discontiguous. The ‘other’ category includes MUG and FAR1 clusters containing both monocots and dicots as well as one cluster containing as its single member the fungal outgroup hop78 (Chalvet et al. 2003). Note that FAR1 family is still in several clusters at this at this level of identity. Figure 2 Relationships between monocot and dicot mudrA genes as determined by phylogenetic analysis, depicted as a majority rule neighbor-joining tree rooted at MULE hop78 (Chalvet et al. 2003). Monocot leaves are labelled in grey, dicot in black. Figure 3 Maximum parsimony tree of the MUG gene family. This majority rule consensus tree is rooted with fungal MULE hop78 (Chalvet et al. 2003). Bootstrap values are shown at nodes. All genes shown are transposon-dissociated mudrA genes (TDMs) and belong to the MUG gene family except for hop78 and At2g07100 and At1g12720 which are transposon-associated mudrA genes (TAMs). Genes indicated by one or two asterisks are associated with ESTs and cDNAs, respectively. Oryza sativa subspecies japonica gene names are shown beginning with “R”, Oryza sativa subspecies indica with “Ri”, Arabidopsis thaliana with “A”, Zea mays with “Z”, Medicago truncatula with “M”, and Populus trichocarpa with “P”. Figure 4 Syntenic 100 kbp region surrounding MUG1 genes. The MUG1 genes are depicted in red. Genes shown with the same shading/pattern share protein-level similarity according to an all-against-all BLASTP search. A color version of this figure is available as supplementary fig. 2. See supplementary table 4 for E values. Vertical lines indicate gaps in the sequence. The Downloaded from http://mbe.oxfordjournals.org/ by guest on July 15, 2013
Medicago sequence represents an unordered contig. Poplar I and II refer, respectively, to the molecules scaffold_201 containing the MUG1 gene eugene3.02010019, and LG_XIII containing the MUG1 gene grail3.0016035401. Note that diagram is not to scale. Downloaded from http://mbe.oxfordjournals.org/ by guest on July 15, 2013
- Page 1 and 2: MUSTANG is a novel family of domest
- Page 3 and 4: Introduction Mobile elements have t
- Page 5 and 6: (www.tigr.org) and from rice build
- Page 7 and 8: For the phylogenetic analysis, CLUS
- Page 9 and 10: Clustering analysis, based on the M
- Page 11 and 12: meristem, and seedling leaves. As a
- Page 13 and 14: Literature Cited Agrawal, A., Q. M.
- Page 15: Lisch, D. 2002. Mutator transposons
- Page 19 and 20: Table 1 The number and distribution
- Page 21 and 22: a MUG FAR1 FAR1 MUG Downloaded from
- Page 23: ice Arabidopsis poplar I poplar II
Figure 1 Relationships between monocot and dicot mudrA <strong>genes</strong> as determined by clustering at<br />
40% identity. The number <strong>of</strong> clusters <strong>of</strong> various sizes <strong>is</strong> shown for monocot (diagonal fill), dicot<br />
(light grey fill) and ‘other’ (dark grey fill). The number <strong>of</strong> MUG (M) and FAR1 (F) clusters <strong>of</strong> a<br />
given size <strong>is</strong> indicated by a number or <strong>is</strong> equal to one where labeled with no number. The<br />
‘Number <strong>of</strong> Clusters’ ax<strong>is</strong> <strong>is</strong> d<strong>is</strong>contiguous. The ‘other’ category includes MUG and FAR1<br />
clusters containing both monocots and dicots as well as one cluster containing as its single<br />
member the fungal outgroup hop78 (Chalvet et al. 2003). Note that FAR1 <strong>family</strong> <strong>is</strong> still in<br />
several clusters at th<strong>is</strong> at th<strong>is</strong> level <strong>of</strong> identity.<br />
Figure 2 Relationships between monocot and dicot mudrA <strong>genes</strong> as determined by phylogenetic<br />
analys<strong>is</strong>, depicted as a majority rule neighbor-joining tree rooted at MULE hop78 (Chalvet et al.<br />
2003). Monocot leaves are labelled in grey, dicot in black.<br />
Figure 3 Maximum parsimony tree <strong>of</strong> the MUG gene <strong>family</strong>. Th<strong>is</strong> majority rule consensus tree<br />
<strong>is</strong> rooted with fungal MULE hop78 (Chalvet et al. 2003). Bootstrap values are shown at nodes.<br />
All <strong>genes</strong> shown are transposon-d<strong>is</strong>sociated mudrA <strong>genes</strong> (TDMs) and belong to the MUG gene<br />
<strong>family</strong> except for hop78 and At2g07100 and At1g12720 which are transposon-associated mudrA<br />
<strong>genes</strong> (TAMs). Genes indicated by one or two aster<strong>is</strong>ks are associated with ESTs and cDNAs,<br />
respectively. Oryza sativa subspecies japonica gene names are shown beginning with “R”,<br />
Oryza sativa subspecies indica with “Ri”, Arabidops<strong>is</strong> thaliana with “A”, Zea mays with “Z”,<br />
Medicago truncatula with “M”, and Populus trichocarpa with “P”.<br />
Figure 4 Syntenic 100 kbp region surrounding MUG1 <strong>genes</strong>. The MUG1 <strong>genes</strong> are depicted in<br />
red. Genes shown with the same shading/pattern share protein-level similarity according to an<br />
all-against-all BLASTP search. A color version <strong>of</strong> th<strong>is</strong> figure <strong>is</strong> available as supplementary fig.<br />
2. See supplementary table 4 for E values. Vertical lines indicate gaps in the sequence. The<br />
Downloaded from<br />
http://mbe.oxfordjournals.org/<br />
by guest on July 15, 2013
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