Supplementary Table S2. Locations of telomere-associated sequences ingenome assembly.
Telomere contig1
/Fosmid(cosmid) clone2
/Contigsmatching fosmid/cosmid sequence3
/ Scaffold(s) / Corresp. to telomere4 / Linkage Group5 / Assembled at end of scaffold?6 / Assembled at end of Chr?7 / Notes81 / 26K20 / 2067, 2147-2150, 2151 / 42
71
72 / ? / ? / yes* / ?
2 / 72H05 / 4, 2, 1538 / 1 / 12 / VI / yes / no / Contig 1538 was assembled at an internal location
3a / 40G17 / 1661,1662 / 19 / 7? / IV / yes / yes** / Contig 1662 ends 25kb from chromosome end
3b / 50E08 / 1661,1662 / 19 / 7 / IV / yes / no / Truncated version of telomere 3a that arose in culture
4 / 41H14 / 1883-1881 / 27 / 5 / III / yes / yes** / Contig 1881 ends 17 kb from chromosome end
5 / 61J04 / (2169) / 81 / 3 / II / yes* / ? / Fosmid sequence composed almost entirely of 18S, 5.8S, 26S ribosomal repeat
6 / (15L20) / 2223, 2195, 2194 / 118
98 / ? / ? / yes* / ?
7 / 69K09 / 1991 / 33 / 14 / VII / yes / yes / Contig ends 9.5 kb from chromosome end
8 / 25N20 / 1531,(1) 2135, 2134 / 17
64 / 2 / I / yes / yes
9 / 41N21 / 1862, 1861 / 26 / 9 / V / yes / yes / Contig ends 4 kb from chromosome end
10 / 56L15
(12I13) / 358, 2110-2103 / 2
51 / ? / I / yes / no / Contig 358 was assembled internally and is possibly duplicated at the telomere
11 / 21N16 / 2120 / 57
(33) / ? / ? / ? / ?
12 / 23E18
(24C14) / 2188, (2200, 2245) / 93
(101,
132) / ? / ? / yes* / ?
13 / 01G11 / (2059) / 40 / 10 / V / yes / yes
14 / 72A13 / 1718, 1717, 1714, 1712, 1711 / 33 / 14 / VII / yes / no / Contigs 1718 through 1711 were assembled in middle of chromosome; contig 1711 ends 6.5 kb from chromosome end
Sequence reads containing chromosome ends were identified among the raw sequence traces by searching for reads containing the telomere repeat motif (TTAGGG)n. The unique sequences proximal to the repeat motif were used to assemble the sequences into telomeric contigs representing each chromosome end. Many of the telomeric reads were derived from fosmid clones whose inserts were derived from chromosome ends. Paired reads generated from the opposite end of the inserts were then retrieved and separately assembled into subtelomeric contigs. Fosmids whose paired reads assembled in subtelomeric contigs containing multiple reads were considered to be nonchimeric and were selected for targeted sequencing of the chromosome ends.
1listed in order of the number of reads in the contig.
2The fosmid clones were created at the Broad Institute. Cosmid clones are listed in brackets and were generated at the University of Kentucky.
3Genomic contigs corresponding to sequences in the fosmid/cosmid inserts are listed in the order centromere -> telomere. Contigs listed in parentheses exhibited imperfect matches to the fosmid/cosmid sequence, indicating the presence of a duplication that was not detected during assembly.
4Based on the chromosomebased, telomere numbering system used by Farman and Leong (1995).
5Based on the chromsome numbering system (Nitta et. al. 1997).
6* indicates that scaffold contains a single contig.
7“?” indicates that the scaffold is not anchored to the genetic map; ** the orientation of these scaffolds was previously unknown but was provided by the telomere data.
8Telomere linked contigs that assembled internally may have been misassembled, or could be sequences that were duplicated but only one copy was incorporated into the assembly.
Farman, M. L. & Leong, S. A. Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea. Genetics140, 479-92 (1995).
Nitta, N., Farman, M. L. & Leong, S. A. Genome organization of Magnaporthe grisea: integration of genetic maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theor. Appl. Genet.95, 20-32. (1997).