Paper Title :In Silico Analysis Reveals Multiple Genes of Mapk, Mapkk and Mapkkk Gene Families of The Mapk Cascade in Nicotiana Tabacum
Author :Hira Iftikhar, Nasar Virk, Xiaofei Cheng, Muhammad F. Bhatti
Article Citation :Hira Iftikhar ,Nasar Virk ,Xiaofei Cheng ,Muhammad F. Bhatti ,
(2016 ) " In Silico Analysis Reveals Multiple Genes of Mapk, Mapkk and Mapkkk Gene Families of The Mapk Cascade in Nicotiana Tabacum " ,
International Journal of Advances in Science, Engineering and Technology(IJASEAT) ,
pp. 42-47,
Volume-4,Issue-3, Spl. Iss-2
Abstract : Tobacco is an important cash crop and model plant studied in detail for mechanisms as fundamental as growth
and development. Mitogen-activated protein kinase (MAPK) cascade constitutes gene families with multiple roles during
plant life in addition to different stress conditions. This study is based on in silico identification, sequence analysis and
phylogenetic analysis of MAPKs retrieved from tobacco genome. A total of 162 MAPK genes, including 30 MAPK, 10
MAPK kinase, and 122 MAPK kinase kinase, were identified from tobacco genome based on similarity and signature motifs.
Prediction of the presence of other domains, motifs and physical properties was performed on the identified MAPKs
followed by multiple sequence alignment-based phylogenetic tree generation. Additional domains were found alongside
protein kinase domain in some of the tobacco MAPKs orthologous to those in Arabidopsis with the same additional
domains.In the identified sequences, variations were observed in the properties – these include gene and protein lengths,
molecular weights, isoelectric points and subcellular localizations. Phylogenetic analysis confirmed clustering of tobacco
MAPKs according to the Arabidopsis MAPK nomenclature.Bootstrap replications were used to determine the reliability of
these results. However, quantitative phylogenetic analysisshowed minute similarities, that too in rare cases, among the
mRNA sequences of the genes in the subject families.
Keywords- NtMAPK, mitogen-activated protein kinase, MKK, MEKK, Raf, ZIK, Phylogenetic tree, heatmap, Plant
Genome.
I. INTRODUCTION
Tobacco is an important cash crop of the Solanaceae
family, an important plant family containing other
crops such as tomato, potato, eggplant and pepper.
Nicotiana tabacum bears tetraploidy which resulted in
larger genome size of tobacco in comparison to other
species in this family [1-3]. With a huge genome size
of approximately 4.5Gb constituting round about
three quarter repeats, tobacco is the result of
Nicotiana sylvestris / Nicotiana tomentosiformis
hybridization [4-6]. Duplication of sequences in the
tobacco genome are thus a result of this
tetraploidization event [7].
Shuffling of DNA via transpositions and reduction in
size via deletions have seen to frequently occur in
allopolyploids [8-10]. Various polyploidization
events in the genus Nicotiana at various times led to
the formation of allotetraploid species which
constitute approximately half of this genus which is
considered to have properties ideal for model studies
on polyploidization [2, 4, 11]. Tobacco is considered
to be a model plant also for alloploidy studies due to
its formation from the ancestral species very recently
about <0.2 million years ago [4, 12]. Allopolyploids
that are young happen to undergo changes in their
genomic compositions widely, with taxa falling in
groups with variations in the extent of changes
occurring in them, starting right after the
hybridization event [13-16].
Looking into the features that count for the
importance of tobacco, the characterization of genes
from the tobacco genome seem to be essential.
Identification of the tobacco genes appear to be a
crucially fundamental step in the process. This study
is based on the identification of mitogen-activated
protein kinases, from the sequenced genome of
commercial tobacco, Nicotiana tabacum, which in
Arabidopsis are known to function in all phases in the
life of the plant [17, 18]. Also known to play central
roles while the plant is in the phase of coping stress
[19-21], whether caused by harsh environmental
conditions or by microbes and insects that result in
phenotypic changes, MAPKs are a center of attention
for the better understanding of plant mechanisms.
MAPK is a large cascade based on families including
Mitogen-activated protein kinases (MPK), Mitogenactivated
protein kinase kinases (MKK), and
Mitogen-activated
Type : Research paper
Published : Volume-4,Issue-3, Spl. Iss-2
DOIONLINE NO - IJASEAT-IRAJ-DOIONLINE-5669
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Published on 2016-10-22 |
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