LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

[V. unguiculata (gene)]
Detail of Experiment mapped on Vigna unguiculata Vu469V1.1

Details

Name	Black-eyed pea gene expression atlas
Description	egume research and cultivar development are important for sustainable food production, especially of high-protein seed. Thanks to the development of deep-sequencing technologies, crop species have been taken to the front line, even without completion of their genome sequences. Black-eyed pea (Vigna unguiculata) is a legume species widely grown in semi-arid regions, which has high potential to provide stable seed protein production in a broad range of environments, including drought conditions. The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24 866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (http://vugea.noble.org), providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation
Contact	The Shanghai Institutes of Biological Sciences – CAS
Xref	PRJNA389300
Reference	Yao S et al . 2016;
Conditions	12
Species	Vigna unguiculata
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	Vu469V1.1
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Genotype	Mutation	Stage	Tissue	Treatment	Level	Time	Samples	Xref	Download alignments
Flower	IT97K-499-35		Flowering	flower				Flower_1 Flower_2 Flower_3	SRR5648395 SRR5648394 SRR5648393	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Leaf	IT97K-499-35		5-week-old plants	leaf				Leaf_1 Leaf_2 Leaf_3	SRR5648392 SRR5648399 SRR5648398	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Mix	IT97K-499-35		5-week-old plants	Mix tissues				Mix_1	SRR5648397	.bam .bai .csi
P10	IT97K-499-35		10 days after pollination	Pod				P10_1	SRR5648391	.bam .bai .csi
P16	IT97K-499-35		16 days after pollination	Pod				P16_1	SRR5648390	.bam .bai .csi
P6	IT97K-499-35		6 days after pollination	Pod				P6_1	SRR5648396	.bam .bai .csi
Root	IT97K-499-35		5-week-old plants	Root				Root_1 Root_2 Root_3	SRR5648382 SRR5648383 SRR5648385	.bam .bai .csi .bam .bai .csi .bam .bai .csi
S10	IT97K-499-35		10 days after pollination	Seed				S10_1 S10_2 S10_3	SRR5648389 SRR5648388 SRR5648381	.bam .bai .csi .bam .bai .csi .bam .bai .csi
S14	IT97K-499-35		14 days after pollination	Seed				S14_1 S14_2 S14_3	SRR5648380 SRR5648376 SRR5648377	.bam .bai .csi .bam .bai .csi .bam .bai .csi
S18	IT97K-499-35		18 days after pollination	Seed				S18_1 S18_2 S18_3	SRR5648378 SRR5648379 SRR5648372	.bam .bai .csi .bam .bai .csi .bam .bai .csi
S8	IT97K-499-35		8 days after pollination	Seed				S8_1 S8_2 S8_3	SRR5648384 SRR5648387 SRR5648386	.bam .bai .csi .bam .bai .csi .bam .bai .csi
Stem	IT97K-499-35		5-week-old plants	Stem				Stem_1 Stem_2 Stem_3	SRR5648373 SRR5648374 SRR5648375	.bam .bai .csi .bam .bai .csi .bam .bai .csi