Maize Genetics Cooperation Newsletter vol 85 2011

 

 

A challenge: who/what/when/where/why are our telomeres?

          --Coe, EH

 

          Telomeres are significant structures -- the maize telomeres doubly so in light of the evolutionary history of the maize genome, and of the many discoveries in maize about cytogenetic behavior, including broken ends, rings, fragments, and the processes of synapsis (N.B. the role of base motifs in other species: Phillips, C. et al., Identification of chromosome sequence motifs that mediate meiotic pairing and synapsis in C. elegans, Nature Cell Biol. 11:934-942, 2009).  We do not yet know enough about maize telomeres.  Mapping genetically and physically would be supportive.

          The updated Genetic 2008 maps in MaizeGDB provide best estimates for coordinates of the telomeres, which I reviewed and revised in September 2010 (Table 1).  The v.2 genome-build erected by Fusheng Wei, presented in WebFPC, was the foundation for placements.  The URL for his expert synthesis of the maize genome is: http://www.genome.arizona.edu/fpc/WebAGCoL/maize/WebFPC/.  Version 1 was used in previous estimates (MNL 83:17) as of October 2008.

          Current placement was inferred in silico from BLAST matches or hybridizations of telomere- specific sequences (e.g., pMTY9ER, pBF266) at one end of a contig, consonant with positions of genetically mapped markers. When these criteria were insufficient, best positions were inferred relative to markers on IBM2.  Improved v.2 placements were defined for the 2S, 3L, 6L, 7L, 7S, and 9S telomeres.  The evidence is strong, though indirect, for map locations of 2L, 3L, 5S, 5L, 6S, 6L, and 9S.  Mapped markers that fall beyond the telomeres are mostly, if not entirely, artifacts of mapping analysis in particular studies. 

          The challenge posed here is much more significant than map coordinates – and more significant than just their physical location and structure and fluidity – it is toward the tools necessary to unveil their functional involvement in central themes of cytogenetics.  Among these themes are evolution of distinct synaptic partners; mechanics of synaptic “finding”; roles of motifs and sequences; and repair of broken ends. 


 

Table 1. Estimated Genetic 2008 map locations of telomeres as of Sep 2010.

 

Name

Ctg

cM

Evidence

telomere1S

1

0

Reviewed Sep 2010 (EHC): Mapped by inference from BLAST of pMTY9ER and pMTY7SC1, associated at the left end of ctg1, and BLAST of subtelomeric clones S46925 S46926 U39641 and U39642 to BAC c0014I07 at left end of ctg1 distal to IBM2 marker umc1354

telomere1L

67

286+/-2

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated from BACs that hybridize with pMTY9ER, located at the end of ctg67 beyond the distal-most markers, anchoring and orienting this contig

telomere2S

485

0

Reviewed Sep 2010 (EHC): Mapped by inference from BLAST of subtelomeric clones S46925 S46926 U39641 and U39642 to BAC b0500C18 in ctg485 at the end of 2S in v.2, and by RFLP placement of bnl(tas1a)

telomere2L

110

183+/-2

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated from the right end of ctg110, distal to IBM2 marker AY111236

telomere3S

111

0

Reviewed Sep 2010 (EHC): Mapped by inference from BAC filter hybridizations of subtelomeric clone U39641(pMTY7SC1) to BACs at the left end of ctg111, distal to umc2118

telomere3L

153

209+/-1

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate revised, estimated from ctg153, placed by IBM2 marker umc1594; ctg152, the next-nearest, has BAC filter hybridizations of pMTY7SC1 and pMTY9ER that are ambiguously distributed

telomere4S

154

0

Reviewed Sep 2010 (EHC): Mapped by inference from BAC filter hybridizations of subtelomeric clones S46925 S46926 U39641 and U39642 to BACs at left end of ctg154, distal to IBM2 marker umc2278

telomere4L

203

189+/-2

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated in silico by inference from BLAST of subtelomeric clones S46925 S46926 U39641 and U39642 to BAC b0528L21 in ctg203 at its right end, distal to IBM2 markers bnlg1890 and umc1707, orienting this contig

telomere5S

204

0

Reviewed Sep 2010 (EHC): Mapped by inference from left end of ctg204, distal to IBM2 marker AI676903

telomere5L

254

173+/-3

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated by inference from the right end of ctg254, distal to IBM2 marker umc1153

telomere6S

256

0

Reviewed Sep 2010 (EHC): Mapped by inference from left end of ctg256, distal to IBM2 markers fdx1, fdx2, and umc2310

telomere6L

291

138+/-2

Reviewed Sep 2010 (EHC): Revised Genetic 2008 coordinate estimated by inference from the right end of ctg291, distal to IBM2 markers hir3 and umc2324

telomere7S

714

0

Reviewed Sep 2010 (EHC): Mapped in silico by inference from BLAST of subtelomeric clones S46926 and U39642 to BAC c0203N21 in ctg714 at the end of 7S in v.2; markers bnl(tas1j), p-pMTY9ER, p-pMTY7SC1 are at the "right" end of ctg714, and IBM2 marker umc2177 is in the adjacent contig, ctg293. 

telomere7L

325

158+/-3

Reviewed Sep 2010 (EHC): Revised Genetic 2008 coordinate estimated by inference from the right end of ctg325, distal to IBM2 marker AY109703

telomere8S

326

0

Reviewed Sep 2010 (EHC): Mapped by inference from left end of ctg326, distal to IBM2 marker csu319

telomere8L

366

160+/-1

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate inferred from BLAST of subtelomeric clones S46925 S46926 U39641 and U39642 to BAC c0447I13 at right end of ctg366, distal to IBM2 marker AY109853

telomere9S

441

0

Reviewed Sep 2010 (EHC): Mapped by inference beyond left end of ctg368, IBM2 markers umc109 and umc1957; ctg441 is placed in v.2 to the left of ctg368 and contains BACs hybridizing with knob probes (i.e., K9S) but has no markers on IBM2 

telomere9L

391

164+/-4

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated by inference from the right end of ctg391, distal to IBM2 markers AW216329, umc1505, and AI901738

telomere10S

392

0

Reviewed Sep 2010 (EHC): Mapped by inference from BAC filter hybridizations of pMTY9ER and pMTY7SC1, associated in parts of ctg392 with the distal-most IBM2 markers, umc48a and others, on 10S

telomere10L

420

136+/-2

Reviewed Sep 2010 (EHC): Genetic 2008 coordinate estimated in silico from BLAST of subtelomeric clones S46925 S46926 U39641 to BAC b0310F06 at the "right" end of ctg420, with BACs that hybridize with pMTY9ER and pMTY7SC1 probes


 

 

 

Maize Genetics Cooperation Newsletter vol 85 2011