scholarly journals Identification and Typing of Malassezia Species by Amplified Fragment Length Polymorphism and Sequence Analyses of the Internal Transcribed Spacer and Large-Subunit Regions of Ribosomal DNA

2004 ◽  
Vol 42 (9) ◽  
pp. 4253-4260 ◽  
Author(s):  
A. K. Gupta ◽  
T. Boekhout ◽  
B. Theelen ◽  
R. Summerbell ◽  
R. Batra
2005 ◽  
Vol 95 (12) ◽  
pp. 1489-1498 ◽  
Author(s):  
Carla D. Garzón ◽  
David M. Geiser ◽  
Gary W. Moorman

Pythium irregulare is a plant-pathogenic oomycete that causes significant damage to a variety of crops, including ornamentals and vegetables. Morphological as well as molecular studies have reported high levels of genetic diversity within P. irregulare sensu lato which has raised the question as to whether it is a single species or is actually a complex of morphologically similar (cryptic) species. In this study, we used amplified fragment length polymorphism (AFLP) fingerprinting and DNA sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal genes (ITS region) and a portion of the mitochondrial cytochrome oxidase II gene and the spacer region between coxI and coxII to characterize 68 isolates of P. irregulare from the United States. The ITS sequence of a P. irregulare neotype at the CBS collection as well as ITS and coxII sequences for P. irregulare, P. spinosum, and P. sylvaticum from previous studies were included in our analysis. Cluster analysis identified a 19-isolate group (IR-II) that separated itself from the rest of the sample (IR-I). Population structure and sequence analyses supported the distinction of IR-I and IR-II and identified IR-II as P. irregulare sensu stricto. IR-I was designated Pythium sp. clade IR-I. Two insertion/deletion mutations and nine nucleotide substitutions in the ITS region and three in the sequence of coxII and the adjacent spacer region separated the two species. Additionally, they differed significantly (P > 0.01) in the frequency of 182 (77%) AFLP alleles. Gene flow results suggested that P. irregulare sensu stricto and Pythium sp. clade IR-I are cryptic species capable of exchanging favorable alleles (Nm = 0.72).


2010 ◽  
Vol 135 (4) ◽  
pp. 341-350 ◽  
Author(s):  
Xiaomeng Li ◽  
Rangjin Xie ◽  
Zhenhua Lu ◽  
Zhiqin Zhou

Citrus species are among the most important fruit trees in the world and have a long cultivation history. However, until now, the exact genetic origins of cultivated Citrus such as sweet orange (Citrus sinensis), lemon (C. limon), and grapefruit (C. paradisi) have remained unidentified. In the present study, amplified fragment length polymorphism (AFLP) fingerprints, nuclear internal transcribed spacer (ITS), and three plastid DNA regions (psbH – petB, trnL – trnF, and trnS - trnG) of 30 accessions of the cultivated citrus and their putative wild ancestors were analyzed in an attempt to identify their paternal and maternal origins. Molecular phylogenetic trees were constructed based on the AFLP data, and chloroplast DNA and ITS sequences using the genus Poncirus as the outgroup. Our results indicated that bergamot (C. aurantifolia) and lemon were derived from citron (C. medica) and sour orange (C. aurantium), and grapefruit was a hybrid that originated from a cross between pummelo (C. grandis) and sweet orange. Rough lemon (C. limon) was probable as a parent of rangpur lime (C. limonia) and guangxi local lemon (C. limonia). Our data also demonstrated that sweet orange and sour orange were hybrids of mandarin (C. reticulata) and pummelo, while rough lemon was a cross between citron and mandarin. For mexican lime (C. aurantifolia), our molecular data confirmed a species of Papeda to be the female parent and C. medica as the male. These findings provide new information for future study on the taxonomy, evolution, and genetic breeding of Citrus.


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