Article Figures & Data
Figures
- FIG. 1.
Linkage distance among 231 Medicago-nodulating rhizobia derived from allelic variation among 10 chromosomal loci. A matrix of the strain identification and the ST followed by the allele labels for each was used in the START (Sequence Type Analysis and Recombinational Tests, version 1.05) program to generate the UPGMA dendrogram. The program was written by Keith Jolley, University of Oxford (14). MLST group affiliation is indicated. Singletons are identified by an “s”; ST numbers followed by a blank belong to group 1.
- FIG. 2.
Population snapshot of 231 Medicago-nodulating rhizobia derived from the allelic variation of 10 chromosomal loci. A matrix of the ST followed by the allele labels for each was used in eBURST (11) to generate a diagram of the evolutionary patterns among the strains. The snapshot was produced by setting the group definition to 0/10 genes. The sizes of the circles are related to the numbers of strains within each ST. The founder and cofounder genotypes are colored blue and red, respectively. Distances between STs indicated by connecting lines are arbitrary.
Tables
- TABLE 1.
Primer sequences for the 10 loci used in MLST analysis of the chromosomes of 231 Medicago-nodulating rhizobia
Locus and primer sequencea Product length (bp) Locus location asd 534 3617313…3618347 F 5<2w9>-CGG CCG GGA GAT GCT GAA CA-3′ R 5′-ATG CGC TTG GTG AAC TTC TTG-3′ edD 552 766634…768454 F 5′-GGC ATC ATC ACC TCC TAC AA-3′ R 5′-CGG CGT GCC GGG ATT-3′ gap 486 2975447…2976457 F 5′-CGG TCC GGT CGA GAC CAA-3′ R 5′-CGG TAG AGA TCC TTG TGC AT-3′ glnD 343 429607…432456 F 5′-GTG CGC TGC CAC ATG CAY TT-3′ R 5′-CCG GRT CRC GCT TGA A-3′ gnd 400 2091007…2092437 F 5′-GGG CCG GCT CAA CTC CTA-3′ R 5′-CGG CAT CGG CAG GTT-3′ nuoE1 293 1381334…1382161 F 5′-GCG CGC KCA GGA GCA GGA-3′ R 5′-CGC AGG CGC CCT GAC ATT-3′ ordL2 456 770925…772211 F 5′-GCG GCG CGG TCG TCA Tx-3′ R 5′-CGC CAT GGC CGG AAT A-3′ recA 357 1948178…1949224 F 5′-CCG GTT CGC TCG GCC TCG ATA-3′ R 5′-CGC CCA TCT CGC CCT CGA TTT-3′ sucA 533 3313082…3316078 F 5′-GCT CGG CCT CGA ATA-3′ R 5′-CCG TCA GCG ACA GGT-3′ zwf 535 769253…770728 F 5′-GGG GGC ACC GGC GAT CTT G-3′ R 5′-AGC GCA GTG CCA TCA GAT TCT-3′ ↵ a F, forward; R, reverse; asd, aspartate-semialdehyde dehydrogenase; edd, phosphogluconate dehydratase; gap, glyceraldehyde 3-phosphate dehydrogenase; glnD, protein-PII uridylyltransferase; gnd, 6-phosphogluconate dehydrogenase; nuoE1, NADH dehydrogenase I chain E protein; ordL2, putative oxidoreductase protein; recA, DNA strand exchange and recombination protein; sucA, 2-oxoglutarate dehydrogenase E1; zwf, glucose-6-phosphate 1-dehydrogenase.
- TABLE 2.
STs with multiple strains
ST Representative straina Strain(s) with the same ST 1 USDA 1002 A145, ATCC 9930, N6B5, 128A9, 3-3, 128A13, 5C6, 17C3, 5A13, M91, M99, M100, 5A10, 5A12, 5B19, 15B65, 15B69, 27-2, 128A8, 54032, LS2A, M68, U45, M94 4 17B6 1322, M248, N6B9, M275, M287, M163, M164, M182, M288, M291, 15A5, M47, M52, M266, M276, M35 5 56A14 USDA 1948, 128A10, 128A14, 15B66, 56A11, 56A13, 128A12, 15B61, 56A4, 56A18, 15B1, 56A2, 56A17 6 74B3 M289, N6B4, 128A6, M101 8 74B12 17C1, N6B6 10 102F85 S14 11 A321 12, CC 169 12 1021 M250, M255, M267, M199, M200, M224, M240, 5B17, M183, M192, 5C15, 19A19, 74B6, 74B14, 311, CC 2003, M11, M5, RCR2011, RF22, S26, M252, M32 13 M7 M204 14 M56 M281 15 M58 M104, M173, M16, M53, M9 30 19A4 19A11, 74B20 31 19A8 17C5, 19A20, N4A2, N4A5, N4A6, N4A8, N4A10, N4A11, 19A16, 74B5, 17A6, 17A7, 19A6, 74B9, B294, L5-30, N4A3, U54 33 M207 M176, M180, M184, M191, M197 34 M210 M202 36 M256 M258, M253, M260, M20, M265 40 Sa-10 V7 44 102F82 M264 46 N4A7 N4A9, N6B3 51 1944 17A8, 17B7, 17C2 60 M76 M105, M165, M292, M6, M44, M49, M50, M201, M21 65 M181 M51 ↵ a USDA 1002 is the type strain for Sinorhizobium meliloti; A321 is the type strain for Sinorhizobium medicae. All other STs consisted of a single strain.
- TABLE 3.
Numbers of alleles and genetic diversity across chromosomes of 231 Medicago-nodulating rhizobia
Locus No. of alleles H asd 16 0.571 edD 18 0.819 zwf 10 0.697 gap 9 0.572 glnD 10 0.731 gnd 8 0.351 nuoE 11 0.450 ordL 9 0.633 recA 10 0.498 sucA 12 0.604 Mean value for total 11.3 0.593 - TABLE 4.
Test of the null hypothesis of linkage equilibrium among 91 multilocus STs in a global collection of 231 Medicago-nodulating rhizobial strainsa
ST(s) included No. of STs Genetic diversity Mismatch variation Standardized I a Monte Carlo P value Reject null hypothesis? Observed Expected All 91 0.59 ± 0.04 7.62 2.24 0.26 0.010 Yes Group 1b 55 0.33 ± 0.07 1.43 1.71 −0.02 0.918 No Groups 5 and 3b 16 0.35 ± 0.09 1.65 1.42 0.02 0.224 No - TABLE 5.
Host plant and geographic origin of Medicago-nodulating rhizobia of the group 1 clonal complex
Founder and cofounder STs included % of rhizobia from host plant of origin Geographic locations of origin (% of rhizobia) M. sativa Annual medics ST-1 ST-10, ST-32, ST-40, ST-42, ST-44, ST-48, ST-52, ST-53, ST-67 73 27 France (5), Jordan (8), Pakistan (38), Syria (16), Nepal (5), exteriora (27) ST-6 ST-14, ST-17, ST-24, ST-26,ST-38, ST-49, ST-88 23 77 Jordan (38), Pakistan (15), Syria (23), Nepal (23) ST-31 ST-46, ST-50, ST-68 92 8 Pakistan (38), Jordan (4), Nepal (42), exterior (16) ST-36 ST-4, ST-20, ST-39, ST-58, ST-62, ST-78, ST-84 12 88 Jordan (50), Pakistan (8), Syria (31), Nepal (4), Turkey (4), exterior (4) ST-60 ST-61, ST-64, ST-65, ST-86 100 Jordan (7), Syria (86), Turkey (7) ST-12 (founder) ST-16, ST-21, ST-22, ST-30, ST-33, ST-34, ST-43, ST-45, ST-56, ST-59, ST-66, ST-83, ST-87, ST-90 43 57 France (2), Jordan (11), Pakistan (23), Syria (26), Nepal (4), Turkey (17), exterior (17) ↵ a Locations exterior to the native range of Medicago include Australia, Canada, Poland, South America, Sweden, and New Zealand.
- TABLE 6.
Symbiotic reaction of several MLEE group B strains, identified as genospecies 2 or Sinorhizobium medicae (21), on Medicago polymorpha a
Strainb MLEE group Host origin Nodule typec Nitrogenase activityd Above-ground plant dry mattere USDA 1002T (ST-1) A M. sativa W 0.08 20 A321T (ST-11) B Medicago truncatula P 1.09 91 CC169 (ST-11) B Medicago rugosa P 1.04 86 M3 (ST-23) B Medicago orbicularis P 1.23 75 M16 (ST-15) B M. orbicularis W/P 0.25 37 M58 (ST-15) B Medicago rotata W 0.01 24 M75 (ST-28) B Medicago radiata W 0.01 12 M161 (ST-63) B Medicago noeana W 0.01 10 M173 (ST-15) B Unspecified W 0.01 16 M254 (ST-74) B M. rotata P 0.91 86 Uninoculated None 0.00 13 ↵ a Results are the means of three replicate jars containing two plants grown for 30 days.
↵ b USDA 1002 and A321 are the type strains for S. meliloti and S. medicae, respectively.
↵ c W, small and white; P, large and pink; W/P, mixture of the two types.
↵ d Acetylene reduction rate is in μmol C2H4/plant/h.
↵ e Dry weight is in mg/plant.
