Authors:Q. Chen, J. Song, W.P. Du, L.Y. Xu, Y. Jiang, J. Zhang, M. Zhang, and G.R. Yu
Chinese endemic wheat landraces possess unique morphological features and desirable traits, useful for wheat breeding. It is important to clarify the relationship among these landraces. In this study, 21 accessions of the four Chinese endemic wheat landrace species were investigated using single-copy genes encoding plastid Acetyl-CoA carboxylase (Acc-1) and 3-phosphoglycerate kinase (Pgk-1) in order to estimate their phylogenetic relationship. Phylogenetic trees were constructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian, and TCS network and gene flow values. The A and B genome sequences from the Pgk-1 loci indicated that three accessions of Triticum petropavlovskyi were clustered into the same subclade, and the T. aestivum ssp. tibetanum and the Sichuan white wheat accessions were grouped into a separate subclade. Based on the Acc-1 gene, T. aestivum ssp. tibetanum and T. aestivum ssp. yunnanense were grouped into one subclade in the A genome; the B genome from T. petropavlovskyi and T. aestivum ssp. tibetanum, and the Sichuan white wheat complex and T. aestivum ssp. tibetanum were grouped in the same clades. The D genome of T. aestivum ssp. yunnanense clustered with T. petropavlovskyi. Our findings suggested that (1) T. petropavlovskyi is distantly related to the Sichuan white wheat complex; (2) T. petropavlovskyi, T. aestivum ssp. tibetanum and T. aestivum ssp. yunnanense are closely related; (3) T. aestivum ssp. tibetanum is closely related to T. aestivum ssp. yunnanense and the Sichuan white wheat complex; and (4) T. aestivum ssp. tibetanum may be an ancestor of Chinese endemic wheat landraces.
Authors:Sz. Stranczinger, A. Borhidi, and J. L. Szentpéteri
Relationships among 16 taxa of Rondeletia complex (Rubiaceae) are estimated using nuclear ribosomal internal transcribed spacer 1 sequence (ITS1). Three species from three more distantly genera in Rondeletieae (one African, two Neotropical) were chosen as outgroup. Previous molecular studies of trnL-F and rps16 data showed that Rondeletia and Rondeletieae are polyphyletic. At present study an alternate set of species were included from Mexico and Central America, and ITS1 was introduced into the molecular analysis, as a new sequence. By analysing of ITS1 region, Arachnothryx, Rondeletia and Rogiera genera were well separated within Rondeletieae tribe.
Authors:S. Naeimi, S. Khodaparast, M. Javan-Nikkhah, C. Vágvölgyi, and L. Kredics
As a first step of a project aimed at the identification of potential biocontrol agents of Rhizoctonia solani, the rice sheath blight fungus, we surveyed the biodiversity of the genus Trichoderma based on sequence of the internal transcribed spacer (ITS) 1 and 2 of the ribosomal RNA gene cluster in paddy fields in Mazandaran province, Northern Iran. Amongst the six obtained species of Trichoderma, T. harzianum and T. virens proved to be the most frequent species in this habitat. Sequence alignment and phylogenetic analysis revealed that the T. harzianum isolates can be divided into 14 different ITS genotypes clustering in four groups. Our results are in agreement with previous molecular studies, which also revealed that T. harzianum is a complex species comprising more or less different ITS genotypes. T. virens was not as diverse as T. harzianum and three different genotypes were distinguished which constituted only one cluster. All T. atroviride and T. hamatum strains had identical ITS sequences.
Authors:S. Talamphai, X.L. Tan, and C. Jantasuriyarat
The coding sequence of starch branching enzyme I gene (SBEI) of 30 rice varieties from China, Laos and Thailand were cloned. All thirty sequences contain 2,463 bp and 14 exons and encode for 820 amino acids. Three sites of Single Nucleotide Polymorphisms (SNPs) A < C, T < C, and T < C were found at positions 1,107, 2,156 and 2,271 in Exon with 6, 13 and 14 respectively. The SNPs at position 1,107 A < C and position 2,271 T < C were silent mutations. The SNP at position 2,156 T < C was a missense mutation and induced a mutation from valine (GTG) to alanine (GCG). Three haplotypes A/T/T, C/T/C and C/C/C were observed. The phylogenetic analysis of 81 SBEI CDS sequences, out of which 30 are from this study and 51 are from previous, classifies them into 2 major groups using 4 sequences as outgroup. The group of monocot comprised of rice, barley, wheat, sorghum whereas maize and the group of dicot comprised of potato, cassava, poplar, Chinese chestnut, bean, legumes and apple. The group of rice SBEI CDS was a major clade in monocot group with high bootstrap value. SBEI gene of rice from China, Laos and Thailand, wheat, apple and poplar contain 14 exons while SBEI gene of rice from Japan and Korea contained only 12 exons. The GC content of SBEI gene of rice varieties was lower than that of wheat and apple but higher than that of poplar.
Authors:Praveen Awasthi, Irshad Ahmad, Sumit Gandhi, and Yashbir Bedi
Rajendrakumar, P., Biswal, A. K., Balachandran, S. M., Sundaram, R. M. (2008) In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogeneticrelationships. In Silico Biol. 8 , 87