Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae

Abstract

Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the approximately 2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions-out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.

Figure 1

M.oryzae telomeres joined to the rDNA array and chromosome-unique sequences. The telomere repeats are represented by small black boxes at the right-hand end of each map. (A) The ribosomal RNA gene array on chromosome II extends all the way to the telomere. The individual repeat units are shown as gray boxes. A MAGGY retroelement insertion is represented as a red box, flanked by smaller boxes representing the LTRs. The orientation of the element is shown with an arrow. (B) The TTAGGG repeats of telomeres 2 and 12 are attached directly to chromosome-unique sequences. White arrows show predicted genes, and the black lines represent intergenic sequences. Transposon insertions are indicated as colored boxes and are distinguished as follows: double-headed arrows = inverted repeat transposons; colored boxes = non-LTR retrotranposons; colored boxes with small boxes at ends = LTR retrotranposons. Arrows inside the boxes represent orientation, and elements shown without an arrowhead and/or tail are truncated versions. The identity of each transposon is noted in the figure. A region of sequence alignment (in opposing orientation) between the two chromosome ends is shown as gray shading connecting the two maps.

Figure 2

Telomeres adjoining a subtelomere region containing a telomere-linked helicase gene. The solid black lines represent a core TLH sequence that is shared by several chromosome ends. The chromosome ends are drawn with the TLH genes (green arrows) aligned to show the extent of subtelomere truncation at each telomere. HARs are shown as white boxes and are labeled in the map of the core TLH region shown at the bottom of the panel. Conserved transposon insertions are shown as colored boxes, and the positions of insertions that are specific to certain ends are noted with downward-pointing arrowheads above the corresponding maps. Chromosome-unique sequences are represented with a dotted line on the left-hand end of each map. Each of the TLH ends has a different sequence in this region. Note that the scales of the maps drawn in panels A, B and C are specific to each panel.

Figure 3

Junction sequences at the boundaries of TLH regions. TLH-associated sequences are shaded gray and chromosome-specific sequences are unshaded. (A) Shows the sequences at region I boundaries. HAR-C repeats units are indicated with arrows. The start of a HAR-D repeat is boxed. (B) Shows sequences spanning the centromere-proximal region II boundaries. Arrows represent tandemly-organized HAR-A motifs.

Figure 4

Variation in HAR organization at different chromosome ends. The HAR sequences listed in Table 1 are depicted in this figure as different-colored rectangles, with each individual rectangle representing a single iteration of a particular repeat sequence, and like-colors representing copies of the same repeat. ^*Additional, highly-mutated HAR-H units are not shown. The identity of each repeat is noted at the top of the figure. The position of each repeat block within its respective subtelomere region is shown in Figure 2C, where it is represented as a white box). Rectangles are drawn to scale, with narrower ones representing incomplete repeat units. The TLH genes are shown as green block arrows, with a gap included to indicate that it is not drawn to scale. The lower panel shows HAR organization in two additional M.oryzae strains.

Figure 5

Transposon insertions in the terminal regions of M.oryzae chromosomes. Shown are the terminal segments of all 14 M.oryzae chromosomes, as represented by the full-length insert in each of the telomeric fosmid clones. Where possible, the sequences are aligned at the starting codon of the TLH ORF (green arrow). Transposable elements are depicted in different ways to illustrate the type of element. Inverted repeat transposons are shown as blue boxes with double-headed arrows. Retrotransposons are illustrated as rectangles, with internal arrows that show orientation. LTR-retrotransposons are drawn as rectangles with small boxes at each end, representing the LTRs. Small boxes that are not attached to rectangles represent solo-LTRs. Colored boxes lacking arrowheads and/or arrowtails correspond to truncated elements. The key at the bottom of the figure shows the color used for each transposon family. For transposon families that contain more than one member element, the identity of the element is noted on the figure (e.g. RETRO5, RETRO6-1, RETRO7-1). Partial elements are not labeled because it was not possible to distinguish between element subfamilies. Asterisks indicate elements showing evidence of having undergone ectopic recombination. Gray areas connecting different chromosome ends represent regions of sequence identity. The scale is shown at the bottom of the figure.

Figure 6

Comparison of transposon density at subtelomeres versus the rest of the genome. The subtelomere regions are defined as the sequences contained in the 14 fosmids. In calculating the percentage of sequence occupied by each element, both full-length and partial copies were considered.