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Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly
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Phytochrome-like genes in the wild plant species
Rhazya stricta
Decne were characterized using a
de novo
genome assembly of next generation sequence data.
Rhazya stricta
contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases. Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids. Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development.
De novo
assembly of the nuclear genome of
R
.
stricta
recovered 45,641 contigs greater than 1000 bp long, which were used in constructing a local database. Five sequences belonging to
Arabidopsis thaliana
phytochrome gene family (i.e.,
AtphyABCDE
) were used to identify
R. stricta
contigs with phytochrome-like sequences using BLAST. This led to the identification of three contigs with phytochrome-like sequences covering
AtphyA
-,
AtphyC
- and
AtphyE
-like full-length genes. Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns. BLASTn and BLASTp results indicated that
RsphyA
mRNA and protein sequences had homologues in
Wrightia coccinea
and and
Solanum tuberosum
, respectively.
RsphyC
-like mRNA and protein sequence were homologous to
Vitis vinifera
and
Vitis riparia
.
RsphyE
-like mRNA coding and protein sequences were homologous to
Ipomoea nil
. Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants. Phylogenetic analysis confirmed that each
R. stricta
phytochrome gene is related to the same phytochrome gene of other flowering plants. It is proposed that the absence of
phyB
gene in
R
.
stricta
is due to
RsphyA
gene taking over the role of
phyB
.
Title: Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly
Description:
Phytochrome-like genes in the wild plant species
Rhazya stricta
Decne were characterized using a
de novo
genome assembly of next generation sequence data.
Rhazya stricta
contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases.
Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids.
Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development.
De novo
assembly of the nuclear genome of
R
.
stricta
recovered 45,641 contigs greater than 1000 bp long, which were used in constructing a local database.
Five sequences belonging to
Arabidopsis thaliana
phytochrome gene family (i.
e.
,
AtphyABCDE
) were used to identify
R.
stricta
contigs with phytochrome-like sequences using BLAST.
This led to the identification of three contigs with phytochrome-like sequences covering
AtphyA
-,
AtphyC
- and
AtphyE
-like full-length genes.
Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns.
BLASTn and BLASTp results indicated that
RsphyA
mRNA and protein sequences had homologues in
Wrightia coccinea
and and
Solanum tuberosum
, respectively.
RsphyC
-like mRNA and protein sequence were homologous to
Vitis vinifera
and
Vitis riparia
.
RsphyE
-like mRNA coding and protein sequences were homologous to
Ipomoea nil
.
Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants.
Phylogenetic analysis confirmed that each
R.
stricta
phytochrome gene is related to the same phytochrome gene of other flowering plants.
It is proposed that the absence of
phyB
gene in
R
.
stricta
is due to
RsphyA
gene taking over the role of
phyB
.
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