Supporting data for "The draft genomes of five agriculturally important African orphan crops"

Dataset type: Genomic, Transcriptomic
Data released on October 16, 2018

Chang Y; Liu H; Liu M; Liao X; Sahu SK; Fu Y; Song B; Cheng S; Kariba R; Muthemba S; Hendre PS; Mayes S; Ho WK; Kendabie P; Wang S; Li L; Muchugi A; Jamnadass R; Lu H; Peng S; Deynze AV; Simons A; Yana-Shapiro H; Xu X; Yang H; Wang J; Liu X (2018): Supporting data for "The draft genomes of five agriculturally important African orphan crops" GigaScience Database. http://dx.doi.org/10.5524/100504

DOI10.5524/100504

A continued growth in the world population is expected to double the worldwide demand for food by 2050. Moreover, 88% of countries are currently facing a serious burden of malnutrition, especially in Africa and Southern & South-Eastern Asia. 30 species alone contribute 95% of the present food energy needs of humans with wheat, maize and rice providing the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition in these countries, a greater utilization of neglected or underused crops (orphan crops) could be a partial solution. Here we present draft genome information from five agriculturally, biologically, medicinally and economically important African orphan crops, namely; Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. The assembled genomes range in size from 217 to 654 Mb. In addition, we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes in V. subterranea, L. purpureus, F. albida, S. birrea and M. oleifera respectively. We have further analyzed the expansion and contraction of selected gene families, and characterized root-nodule-symbiosis genes, transcription factors and starch biosynthesis related genes in these genomes. This genome data will be useful to identify and characterize agronomically important genes and understand their mode of actions, enabling genomics-based, evolutionary studies, and breeding strategies for designing faster, focused and predictable crop improvement programs.

Additional details

Read the peer-reviewed publication(s):

Chang, Y., Liu, H., Liu, M., Liao, X., Sahu, S. K., Fu, Y., … Liu, X. (2018). The draft genomes of five agriculturally important African orphan crops. GigaScience, 8(3). doi:10.1093/gigascience/giy152

Related datasets:

doi:10.5524/100504 HasPart doi:10.5524/101054
doi:10.5524/100504 HasPart doi:10.5524/101055
doi:10.5524/100504 HasPart doi:10.5524/101056
doi:10.5524/100504 HasPart doi:10.5524/101057
doi:10.5524/100504 HasPart doi:10.5524/101058

Additional information:

www.africanorphancrops.org

Accessions (data generated as part of this study):

BioProject: PRJNA453822
BioProject: PRJNA474418

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Faidherbia_albida_dry_seed138055  Faidherbia albida Description:RNA extracted from dry seed of Faidher...
Alternative names:apple-ring acacia
Alternative accession-BioSample:SAMN08991390
...
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Faidherbia_albida_leaf138055  Faidherbia albida Description:Genomic DNA extracted from leaf of a F...
Alternative names:apple-ring acacia
Alternative accession-BioSample:SAMN08991339
...
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Faidherbia_albida_leaf_bud138055  Faidherbia albida Description:RNA extracted from leaf bud of Faidher...
Alternative names:apple-ring acacia
Alternative accession-BioSample:SAMN08991391
...
+
Faidherbia_albida_stem138055  Faidherbia albida Description:RNA extracted from stem of Faidherbia ...
Alternative names:apple-ring acacia
Alternative accession-BioSample:SAMN08991392
...
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Faidherbia_albida_young_leaf138055  Faidherbia albida Description:RNA extracted from young leaf of Faidh...
Alternative names:apple-ring acacia
Alternative accession-BioSample:SAMN08991393
...
+
Lablab_purpureus_leaf35936antaque Lablab purpureus Description:Genomic DNA extracted from leaf of a L...
Alternative names:hyacinth bean
Alternative accession-BioSample:SAMN09355696
...
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Lablab_purpureus_petal35936antaque Lablab purpureus Description:RNA extracted from petal of Lablab pur...
Alternative names:hyacinth bean
Alternative accession-BioSample:SAMN09355999
...
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Lablab_purpureus_sepal35936antaque Lablab purpureus Description:RNA extracted from sepal of Lablab pur...
Alternative names:hyacinth bean
Alternative accession-BioSample:SAMN09356001
...
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Lablab_purpureus_stem35936antaque Lablab purpureus Description:RNA extracted from stem of Lablab purp...
Alternative names:hyacinth bean
Alternative accession-BioSample:SAMN09356000
...
+
Lablab_purpureus_young leaf35936antaque Lablab purpureus Description:RNA extracted from young leaf of Labla...
Alternative names:hyacinth bean
Alternative accession-BioSample:SAMN09356002
...
+
Displaying 1-10 of 23 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Phylogenetic treeUNKNOWN0.82 KB2018-09-07
Phylogenetic treeUNKNOWN10.94 KB2018-09-07
ReadmeTEXT2.88 KB2018-09-07
otherFASTA70.49 KB2018-09-07
otherFASTA809.88 KB2018-09-07
Phylogenetic treeUNKNOWN0.42 KB2018-09-07
Displaying 1-6 of 6 File(s).
Funding body Awardee Award ID Comments
Shenzhen Municipal Government of China No. JCYJ20150831201643396
Shenzhen Municipal Government of China No. JCYJ20150529150409546
State Key Laboratory of Agricultural Genomics No. 2011DQ782025
Guangdong Provincial Key Laboratory of Genome Read and Write No. 2017B030301011
Date Action
October 16, 2018 Dataset publish
December 3, 2018 Manuscript Link added : 10.1093/gigascience/giy152
December 4, 2018 Relationship updated : DOI 101058