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Legume Genomics and Genetics 2014, Vol.5, No.7, 1-7
Research Report Open Access
De Novo RNA Seq Assembly and Annotation of
Trigonella foenum-graecum
Sagar S. Patel
, Dipti B. Shah
, Hetalkumar J. Panchal
1. G. H. Patel Post Graduate Department of Computer Science and Technology, Sardar Patel University, Vallabh Vidyanagar, Gujarat-388120, India
2. Gujarat Agricultural Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat- 395007, India
Corresponding author email:
Legume Genomics and Genetics, 2014, Vol.5, No.7 doi: 10.5376/lgg.2014.05.0007
Received: 22 Oct., 2014
Accepted: 13 Nov., 2014
Published: 19 Dec., 2014
2014 Patel et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Patel et al., 2014, De Novo RNA Seq Assembly and Annotation of
Trigonella foenum-graecum
L. (SRR066197), Legume Genomics and Genetics, Vol.5, No.7
7 (doi:
Trigonella foenum-graecum
commonly known as fenugreek, is a small seeded annual dicotyledonous legume
belonging to the subfamily
Trigonella foenum-graecum
is one of the oldest medicinal plants
Different parts of the plant such as leaves and seeds are used for many purposes in India. Recently, next-generation sequencing
technology, termed RNA-seq, has provided a powerful approach for analysing the transcriptome. This study is focus on RNA-seq of
Trigonella foenum-graecum
L. of
from NCBI database for de novo Transcriptome analysis. A total of 627,117 million
single reads were generated with N50 of 470 bp. Sequence assembly contained total 7256 contigs which is further searched with
known proteins and a total of 2258 genes were identified. Among these, only 192 unigenes were annotated with 10179 gene ontology
(GO) functional categories and sequences mapped to 87 pathways by searching against the Kyoto Encyclopedia of Genes and
Genomes pathway database (KEGG). These data may be useful for gene discovery and functional studies and the large number of
transcripts reported in the current study will serve as a valuable genetic resource of the
Trigonella foenum-graecum
Transcriptome; Bioinformatics;
Trigonella foenum-graecum
L. is an annual,
leguminous plant. It has tri-foliate, obovate and
toothed, light green leaves. Its stems are erect, long
and tender. Blooming period occurs during summer.
Flowers are yellow-white, occurring singly or in pairs
at the leaf axils. Fruit is a curved seed-pod, with ten to
twenty flat and hard, yellowish-brown seeds. They are
angular- rhomboid, oblong or even cubic, and have a
deep furrow dividing them into two unequal lobes.
One of the main uses of this plant is as Medicinal use
like, It has been used for centuries for different female
conditions, brain and nervous system ailments, skin,
liver and metabolic disorders. It is also considered
highly beneficial for respiratory and gastrointestinal
It is a highly potent female herb, since it helps
relaxing the uterus and relieving menstrual pains, and
is an excellent stimulator of milk production in
nursing mothers; for the gastrointestinal tract,
Trigonella foenum-graecum
is usually suggested in
treatments of poor digestion, gastric inflammations,
enteritis, especially for convalescents. It can also be
used in cases of weight loss, poor appetite and even in
treatment of anorexia nervosa. Different blood
conditions, such as anemia, and nervous system
disorders (neurasthenia) can also be successfully
treated with
Trigonella foenum-graecum
L. and for the
respiratory conditions,
Trigonella foenum-graecum
is excellent in treatment of bronchitis, mucous
congestions, different infections, tuberculosis.
Next generation sequencing methods for high
throughput RNA sequencing (transcriptome) is
becoming increasingly utilized as the technology of
choice to detect and quantify known and novel
transcripts in plants. This Transcriptome analysis
method is fast and simple because it does not require
cloning of the cDNAs. Direct sequencing of these
cDNAs can generate short reads at an extraordinary
depth. After sequencing, the resulting reads can be
assembled into a genome-scale transcription profile. It
is a more comprehensive and efficient way to measure
Transcriptome composition, obtain RNA expression