Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth–death, birth–death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.
This chapter deals with major endemic and emerging fungal diseases of citrus as well as with exotic fungal pathogens potentially harmful for citrus industry in the Mediterranean region, with particular emphasis on diseases reported in Italy and Maghreb countries. The aim is to provide an update of both the taxonomy of the causal agents and their ecology based on a molecular approach, as a preliminary step towards developing or upgrading integrated and sustainable disease management strategies. Potential or actual problems related to the intensification of new plantings, introduction of new citrus cultivars and substitution of sour orange with other rootstocks, globalization of commerce and climate changes are discussed. Fungal pathogens causing vascular, foliar, fruit, trunk and root diseases in commercial citrus orchards are reported, including Plenodomus tracheiphilus, Colletotrichum spp., Alternaria spp., Mycosphaerellaceae, Botryosphaeriaceae, Guignardia citricarpa and lignicolous basidiomycetes. Diseases caused by Phytophthora spp. (oomycetes) are also included as these pathogens have many biological, ecological and epidemiological features in common with the true fungi (eumycetes).
Appropriate knowledge of genetic variation and mating systems is necessary to optimise conservation and utilisation of genetic resources. The present study provides estimates of mating system parameters in three natural populations of Hedysarum coronarium, using isozyme markers. There was no detectable variation among populations of single-and multilocus outcrossing rates (t s , t m), which did not differ significantly from complete outcrossing. However, in pooled populations, estimates of t s (0.820 ± 0.073) and t m (0.830 ± 0.069) were both significantly different from the unity. The fixation index (F) and the biparental inbreeding rate, given by the difference between t m and t s , were not significantly different from zero. t m and t s , estimated at the seedling stage, were both smaller than those determined at the adult phase, indicating some inbreeding depression acting between these two stages. Hedysarum coronarium / isozyme / mating system / outcrossing rate Résumé-Estimation des paramètres du régime de reproduction chez Hedysarum coronarium L. (Légumineuse, Fabacée). La connaissance de la variation génétique et des modes de reproduction est nécessaire à l'optimisation de la conservation et l'utilisation des ressources génétiques. Cette étude fournit des estimations du régime de reproduction dans trois populations naturelles d'Hedysarum coronarium L., au moyen de marqueurs isoenzymatiques. L'analyse montre que les taux d'allogamie uni-et multilocus (t s , t m) présentent de faibles variations entre populations sans qu'ils ne s'écartent significativement de l'allogamie complète. Toutefois, pour l'ensemble des populations, t s (0.820 ± 0.073) et t m (0.830 ± 0.069) sont tous deux significativement différents de l'allogamie totale (t = 1.0). L'indice de fixation (F) et le taux de croisements consanguins, donné par la différence entre t m et t s , ne sont pas significativement différents de zéro. t m et t s , estimés sur des plantes au stade juvénile, sont inférieurs à ceux obtenus au stade adulte, suggérant l'existence d'une dépression de consanguinité agissant entre la germination des graines et la maturité des plantes. Hedysarum coronarium / isozyme / régime de reproduction / taux d'allogamie
Par l'observation de la couleur des fleurs dans des descendances de pollinisation naturelle et de croisements chez Hedysarum coronarium L., on montre que l'allopollen est tellement favorisé par rapport à l'autopollen que 90 p. 100 des graines sont issues d'une fécondation croisée. L'étude de la compétition pollinique chez cette espèce montre également que les gènes de coloration a et b ne semblent pas avoir une liaison particulière avec un gène gamétophytique mâle. Mots clés additionnels : Autogamie, allogamie, pollinisation naturelle, pollinisation artificielle, pollinisation pluripaternelle, gène de coloration, eompétition gamétique. SUMMARY Study of pollen competition in sulla (Hedysarum coronarium L., Leguminosae) The character « prcscnce-absencc of flower anthocyanins was used as a genetic marker in the study of pollen competition in sulla (Hedysarum coronarium L.). This species was shown to be preferentially allogamous. The rate of allogamy obtained under natural and artificial pollinisation was close to 90 %. The use of different sorts of pollen in simple crosses without castration and in multipaternal pollination experiments showed that the two flower colour genes, a and b, were not apparently linked to a male gametophyte gene.
Isolates from root nodules of Hedysarum flexuosum, sampled from north region of Algeria, were analyzed on the basis of their phenotypic and molecular characteristics. They were tested for their tolerance to NaCl, pH, temperatures, antibiotics and heavy metals resistance. Interestingly, the isolate Hf_04N appeared resistant to ZnCl2 (50 μg/mL) and grew at high saline concentration up to 9 %. The phylogenetic positions of five isolates were studied by comparative sequence analysis of 16S rRNA, recA, nifH and nodD genes. There were grouped close to the Rhizobium sullae type strain in relation to their 16S rRNA, recA and nifH genes-based phylogenies. By contrast, the tree of nodD gene was not congruent with ribosomal, housekeeping and nitrogen fixation genes. We suggest that our strains have a novel nodD gene. The detection of conserved domains of NodD protein and nitrogenase reductase enzyme, confirm their ability to nodulate and fix nitrogen.
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