MOLECULAR PHYLOGENY AND STRUCTURE PREDICTION OF RICE RFT1 PROTEIN

2016 ◽  
Vol 78 (2) ◽  
Author(s):  
Shahkila Mohd Arif ◽  
Abdulrahman Mahmoud Dogara ◽  
Nyuk Ling Ma ◽  
Mohd Shahir Shamsir Omar ◽  
Sepideh Parvizpour ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Sequence Data ◽  
World Population ◽  
Data Sets ◽  
Important Species ◽  
The Family ◽  
Close Relationship ◽  
Protein Sequence Data ◽  
Flowering Time Gene ◽  
Mp Method

Rice is one of the most important species in the family of Poaceae. As one of the major crop that is consumed by world population, it is cultivated commercially in many parts of the world. Hence, the phylogeny study of this crop is crucial as a step for improvement of its breeding programs. Phylogenetic relationship among 12 rice cultivars that originated from two common sub-species; Indica and Japonica were inferred by comparing protein sequence data sets derived from its flowering time gene, namely RFT1 and analyzed using maximum parsimony (MP) method. The predicted structure of RFT1 protein was generated by I-TASSER server and analyzed using YASARA software. The result showed that the cultivars were classified into two major groups, where the first group (Japonica) evolved first followed by the second group (Indica). The findings suggested that some cultivars had a close relationship with each other even it is originates from different varieties. The relationships among these cultivars provide useful information for better understanding of molecular evolution process and designing good breeding program in order to generate new cultivar.

scholarly journals Phylogeny of the Serpin Superfamily: Implications of Patterns of Amino Acid Conservation for Structure and Function

2000 ◽  
Vol 10 (12) ◽  
pp. 1845-1864
Author(s):  
James A. Irving ◽  
Robert N. Pike ◽  
Arthur M. Lesk ◽  
James C. Whisstock
Keyword(s):  
Sequence Data ◽  
Initial Point ◽  
Structure And Function ◽  
Conserved Residues ◽  
Consensus Analysis ◽  
The Family ◽  
Protein Sequence Data ◽  
And Function ◽  
Conserved Amino Acids ◽  
Genome Projects

We present a comprehensive alignment and phylogenetic analysis of the serpins, a superfamily of proteins with known members in higher animals, nematodes, insects, plants, and viruses. We analyze, compare, and classify 219 proteins representative of eight major and eight minor subfamilies, using a novel technique of consensus analysis. Patterns of sequence conservation characterize the family as a whole, with a clear relationship to the mechanism of function. Variations of these patterns within phylogenetically distinct groups can be correlated with the divergence of structure and function. The goals of this work are to provide a carefully curated alignment of serpin sequences, to describe patterns of conservation and divergence, and to derive a phylogenetic tree expressing the relationships among the members of this family. We extend earlier studies by Huber and Carrell as well as by Marshall, after whose publication the serpin family has grown functionally, taxonomically, and structurally. We used gene and protein sequence data, crystal structures, and chromosomal location where available. The results illuminate structure–function relationships in serpins, suggesting roles for conserved residues in the mechanism of conformational change. The phylogeny provides a rational evolutionary framework to classify serpins and enables identification of conserved amino acids. Patterns of conservation also provide an initial point of comparison for genes identified by the various genome projects. New homologs emerging from sequencing projects can either take their place within the current classification or, if necessary, extend it.

Phylogeny of the Parmeliaceae–DNA Data Versus Morphological Data

1998 ◽  
Vol 30 (4-5) ◽  
pp. 463-472 ◽  
Author(s):  
Jan-Eric Mattsson ◽  
Mats Wedin
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Slight Variation ◽  
Hypogymnia Physodes ◽  
Nuclear Rdna ◽  
Future Studies ◽  
The Family ◽  
Rdna Sequence Data ◽  
Close Relationship

AbstractIn order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

scholarly journals Song and Molecular Data Identify Congruent but Novel Affinities of the Green Oropendola (Psarocolius Viridis)

The Auk ◽  
2004 ◽  
Vol 121 (1) ◽  
pp. 224-229
Author(s):  
J. Jordan Price ◽  
Scott M. Lanyon
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Sets ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Morphological Differences ◽  
Vocal Evolution ◽  
Avian Song

Abstract The accuracy with which avian song features indicate phylogenetic relationships has rarely been investigated. In a previous study of vocal evolution in oropendolas (Price and Lanyon 2002a), we estimated the phylogenetic position of the Green Oropendola (Psarocolius viridis) using characters derived from oropendolas' elaborate courtship songs. Here, we test that estimate using mitochondrial DNA sequence data. The position of the Green Oropendola determined from molecular data is remarkably close to that based solely on song characters; both data sets support a close relationship between P. viridis and members of the genus Gymnostinops. Numerous morphological differences yet low genetic divergence among the species in question suggest that rapid diversification has occurred in the group. The fact that this position has not been proposed previously for P. viridis underscores the effectiveness of song characters for phylogenetic reconstruction.

Universal trees based on large combined protein sequence data sets

10.1038/90129 ◽  
2001 ◽  
Vol 28 (3) ◽  
pp. 281-285 ◽  
Author(s):  
James R. Brown ◽  
Christophe J. Douady ◽  
Michael J. Italia ◽  
William E. Marshall ◽  
Michael J. Stanhope
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Data Sets ◽  
Protein Sequence Data

scholarly journals Partitioning clustering algorithms for protein sequence data sets

2009 ◽  
Vol 2 (1) ◽  
Author(s):  
Sondes Fayech ◽  
Nadia Essoussi ◽  
Mohamed Limam
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Clustering Algorithms ◽  
Data Sets ◽  
Protein Sequence Data

scholarly journals High Performance Pattern Matching on Heterogeneous Platform

2014 ◽  
Vol 11 (3) ◽  
pp. 88-98 ◽  
Author(s):  
Shima Soroushnia ◽  
Masoud Daneshtalab ◽  
Juha Plosila ◽  
Tapio Pahikkala ◽  
Pasi Liljeberg
Keyword(s):  
Pattern Matching ◽  
High Performance ◽  
Sequence Data ◽  
Good Choice ◽  
Data Sets ◽  
Biological Sequence ◽  
Computational Molecular Biology ◽  
Heterogeneous Architectures ◽  
Protein Sequence Data ◽  
Gpu Architecture

Summary Pattern discovery is one of the fundamental tasks in bioinformatics and pattern recognition is a powerful technique for searching sequence patterns in the biological sequence databases. Fast and high performance algorithms are highly demanded in many applications in bioinformatics and computational molecular biology since the significant increase in the number of DNA and protein sequences expand the need for raising the performance of pattern matching algorithms. For this purpose, heterogeneous architectures can be a good choice due to their potential for high performance and energy efficiency. In this paper we present an efficient implementation of Aho-Corasick (AC) which is a well known exact pattern matching algorithm with linear complexity, and Parallel Failureless Aho-Corasick (PFAC) algorithm which is the massively parallelized version of AC algorithm without failure transitions, on a heterogeneous CPU/GPU architecture. We progressively redesigned the algorithms and data structures to fit on the GPU architecture. Our results on different protein sequence data sets show that the new implementation runs 15 times faster compared to the original implementation of the PFAC algorithm.

scholarly journals Phylogenetic analysis of ITS sequences suggests a Pliocene origin for the bipolar distribution of Scleranthus (Caryophyllaceae)

2003 ◽  
Vol 16 (3) ◽  
pp. 301 ◽  
Author(s):  
R. D. Smissen ◽  
P. J. Garnock-Jones ◽  
G. K. Chambers
Keyword(s):  
Sequence Data ◽  
Its Sequence ◽  
Data Sets ◽  
Long Distance Dispersal ◽  
Lineage Sorting ◽  
Long Distance ◽  
The Family ◽  
Alternative Hypotheses ◽  
Bipolar Distribution ◽  
Recent Origin

Scleranthus is a genus of about 12 species of herbaceous plants or subshrubs native to Eurasia and Australasia. Here Scleranthus is shown to consist of European and Australasian clades, which diverged within the last 10 million years. Biogeographic implications of this dating and alternative hypotheses explaining the disjunct north–south distribution of the genus, are discussed. The trans-Tasman distributions of S. biflorus and S. brockiei are of recent origin and therefore consistent with long-distance dispersal rather than vicariance explanations. Morphological and ITS sequence data sets are significantly incongruent and trees derived from them differ over relationships among Australasian species. Hybridisation and introgression or lineage sorting are invoked to explain this discordance. Within the family Caryophyllaceae, Scleranthus ITS2 sequences have greater similarity to sequences from representatives of the subfamilies Alsinoideae and Caryophylloideae than to sequences from representatives of the subfamily Paronychioideae.

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