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. 2019 Mar 1;8(3):giy152.
doi: 10.1093/gigascience/giy152.

The draft genomes of five agriculturally important African orphan crops

Yue Chang  1   2 , Huan Liu  1   2   3 , Min Liu  1   2   3 , Xuezhu Liao  1   2   3 , Sunil Kumar Sahu  1   2   3 , Yuan Fu  1   2 , Bo Song  1   2 , Shifeng Cheng  1   2 , Robert Kariba  4 , Samuel Muthemba  4 , Prasad S Hendre  4 , Sean Mayes  5   6   7 , Wai Kuan Ho  6   7 , Anna E J Yssel  8 , Presidor Kendabie  5 , Sibo Wang  1   2 , Linzhou Li  1   2 , Alice Muchugi  4 , Ramni Jamnadass  4 , Haorong Lu  1   2 , Shufeng Peng  1   2 , Allen Van Deynze  4   9 , Anthony Simons  4 , Howard Yana-Shapiro  4   9 , Yves Van de Peer  10   11   8 , Xun Xu  1   2 , Huanming Yang  1   2 , Jian Wang  1   2 , Xin Liu  1   2   3   12
Affiliations

The draft genomes of five agriculturally important African orphan crops

Yue Chang et al. Gigascience. .

Abstract

Background: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution.

Results: Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes.

Conclusions: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Keywords: food security; orphan crops; root nodule symbiosis; transcription factor; transcriptome; whole-genome sequencing.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1:
Figure 1:
Phylogenetic and evolutionary analysis. Values at branch points indicate estimates of divergence time (million years ago [Mya]); blue numbers show divergence time (Mya); red nodes indicate previously published calibration times. V. sub shows seeds of Vigna subterranea; L. pur, flowers of Lablab purpureus; F. alb, seed pods of Faidherbia albida; S. bir, fruit of Sclerocarya birrea; andM. ole, flowers of Moringa oleifera. Scale bar = 10 million years.
Figure 2:
Figure 2:
The groups of orthologs shared by the orphan crops. (A) Groups of orthologs shared between Lablab purpureus (L. pur), Faidherbia albida (F. alb), Glycine max (G. max), Medicago truncatula (M. tru), and Vigna subterranea (V. sub). (B) Groups of orthologs shared between Sclerocarya birrea (S. bir), Moringa oleifera (M. ole), Carica papaya (C. pap), Citrus sinensis (C. sin), and Theobroma cacao (T. cac). Venn diagram generated using [60].
Figure 3
Figure 3
Percentages of transcription factors in five orphan species. Blastp was used to search against 58 plant transcription factor families obtained from PlantTFDB [70] (see Additional file 2: Table S14). In this figure, MADS includes M-type_MADS and MIKC_MADS. MYB includes MYB and MYB_related. NF-YA/B/C includes NF-YA, NF-YB and NT-YC. “Others” comprises 31 types of transcription factors (E2F/DP, Nin-like, TALE, YABBY, GeBP, BES1, DBB, CO-like, CPP, SBP, STAT, WOX, BBR-BPC, CAMTA, AP2, ZF-HD, S1Fa-like, ARR-B, SRS, GRF, LSD, NF-X1, EIL, RAV, HRT-like, HB-PHD, VOZ, Whirly, SAP, LFY and NZZ/SPL) whose percentage was less than 1%.
Figure 4:
Figure 4:
Identification of genes involved in the starch biosynthesis pathway. Genes identified as being involved in starch synthesis are shown in red. Numbers of homolog genes are presented in Additional file 1: Table S11. AGP, ADP-glucose pyrophosphorylase; AGPL, AGP large subunit; AGPS, AGP small subunit; PHOH, starch phosphorylase H (cytosolic type); GBSS, granule-bound starch synthase; SS, soluble starch synthase; BE, starch branching enzyme; ISA, isoamylase; DPE, starch debranching enzyme.
Figure 5:
Figure 5:
The common symbiosis signaling pathway among the orphan crops. Sixteen root nodulation symbiosis signal (Sym) pathway genes were identified in three legumes (Vigna subterranea, Lablab purpureus, and Faidherbia albida) and two non-legumes (Sclerocarya birrea and Moringa oleifera). Lj, Lotus japonicus; Mt, Medicago truncatula; LCOs, Lipochitooligosaccharides.
See this image and copyright information in PMC

Comment in

  • Sequencing forgotten crops.
    Tena G. Tena G. Nat Plants. 2019 Jan;5(1):5. doi: 10.1038/s41477-018-0354-z. Nat Plants. 2019. PMID: 30626921 No abstract available.

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