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The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is believed to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops including Solanum melongena. Breeding of S. aethiopicum has lagged behind due to lack of genomic resources.
We assembled a 1.02 Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (76.2%). We annotated 37,681 gene models including 34,906 protein-coding genes. We observed an expansion of disease resistance genes through two rounds of amplification of long terminal repeat retrotransposons (LTR-Rs), which may have occurred around 1.25 and 3.5 million years ago, respectively. We identified 14,995,740 SNPs by re-sequencing 65 S. aethiopicum and S. anguivi genotypes, of which 41,046 SNPs were closely linked to disease resistance genes. The domestication and demographic history analysis revealed the active selection for genes involved in drought tolerance in both Gilo and Shum groups. A pan-genome of S. aethiopicum with a total of 51,351 protein-coding genes was assembled, 7,069 genes of which are missing in the reference genome.
The genome sequence of S. aethiopicum enhances our understanding of its extraordinary biotic and abiotic resistance nature. The SNPs identified will be available for immediate use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.

Discaria trinervis (D. trinervis) is a nodulating species belonging to the Rosales order. It is nodulated by Frankia bacteria, native from South America, found from 31º to 48º S. DNA was collected from leaves of 2 to 4-month-old plants grown in a greenhouse. We sequenced the genome to a depth of approximately 294X. The assembled scaffolds of high quality sequences total 310MB, with the contig and scaffold N50 values of 27kb and 115kb respectively. We identified 32,886 protein-coding genes with a mean length of 1.206kb.

Faidherbia albida is an agriculturally, biologically, medicinally and economically important African orphan crop. It is a thorny tree growing up 630 m (2098 ft) tall and 2 m (6.6 ft) in trunk diameter. Its deep-penetrating tap root makes it highly resistant to drought. The bark is grey, and fissured when old. There are 11,000 seeds/kg. Wikipedia includes in its list of uses; flowers are important in raising bees; seed pods important for raising livestock and as food sources for camel, elephant, antelope, buffalo, baboons and others; Ashes of the wood are used in making soap and as a depilatory and tanning agent for hides; Wood is used for canoes, mortars, and pestles, and carving; the thorny branches useful for a natural barbed fence.
Here we present draft genome information of Faidherbia albida. The assembled genome of Faidherbia albida is 654 Mb, and we predict 28979 protein-coding genes for this crop species. 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 the genome of this species.

Vigna subterranea is an agriculturally, biologically, medicinally and economically important African orphan crop. Bambara Groundnut grows well any where groundnut (peanut) grows and so is vastly present from Kwara state and throughout the northern parts of Nigeria.
Wikipedia states that the Bambara groundnut represents the third most important grain legume in semi-arid Africa. It is resistant to high temperature and is suitable for marginal soils where other leguminous crops cannot be grown. Wikipedia includes in its list of uses; the seeds are used for food and beverages; the entire plant is known for soil improvement; in West Africa, the nuts are eaten as a snack, roasted and salted, processed into cake, or as a meal, boiled similar to other beans.
Here we present draft genome information of Vigna subterranea. The assembled genome of Vigna subterranea is 535 Mb, and we predict 31707 protein-coding genes for this crop species. 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 the genome of this species.

Lablab purpureus is an agriculturally, biologically, medicinally and economically important African orphan crop. Wikipedia states L. purpureus is variable due to extensive breeding in cultivation, but in general they are annual or short-lived perennial vines. The fruit is a legume pod variable in shape, size, and colour. It is usually several cm long and bright purple to pale green and contains up to four seeds. The seeds are white, brown, red, or black depending on the cultivar, sometimes with a white hilum. Wild plants have mottled seeds. The seed is about a cm long.
Wikipedia includes in its list of uses; the fruit and beans are edible if boiled well with several changes of the water; the leaves are eaten raw or cooked like spinach; the flowers can be eaten raw or steamed; the root can be boiled or baked for food and the seeds are used to make tofu and tempeh.
In Kenya, the bean is though to encourage lactation and has historically been the main dish for breastfeeding mothers.Here we present draft genome information of Lablab purpureus. The assembled genome of Lablab purpureus is 395 Mb, and we predict 20946 protein-coding genes for this crop species. 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 the genome of this species.

Sclerocarya birrea is an agriculturally, biologically, medicinally and economically important African orphan crop.
The tree is a single stemmed tree with a wide spreading crown. It is characterised by a grey mottled bark. The tree grows up to 18m tall mostly in low altitudes and open woodlands. The fruits, which ripen between December and March, have a light yellow skin, with white flesh that is rich in vitamin C.
Wikipedia includes in its list of uses; the fruit is used for food in Africa; the tree produces a high quality cooking oil; on an industrial level the fruit is processed where pulp, pips, kernels and kernal oil are extracted and stored for processing. The fruit is also used to make the cream liqueur Amarula, and the oil used in cosmetics.
Here we present draft genome information of Sclerocarya birrea. The assembled genome of Sclerocarya birrea is 331 Mb, and we predict 18937 protein-coding genes for this crop species. 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 the genome of this species.

Moringa oleifera is an agriculturally, biologically, medicinally and economically important African orphan crop. Wikipediastates M. oleifera is a fast-growing, drought-resistant tree, native to the southern foothills of the Western Ghats in southwestern India, and widely cultivated in tropical and subtropical areas where its young seed pods and leaves are used as vegetables, and many parts of the tree are used in traditional herbal medicine. It can also be used for water purification and hand washing.
Moringa trees have been used to combat malnutrition, especially among infants and nursing mothers.Moringa has numerous applications in cooking throughout its regional distribution. The fruits or seed pods, known as drumsticks, are a culinary vegetable commonly used in soups and curries. The leaves are also commonly eaten with many culinary uses, and the flowers are featured in some recipes as well.
Here we present draft genome information of Moringa oleifera. The assembled genome of Moringa oleifera is 217 Mb, and we predict 18451 protein-coding genes for this crop species. 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 the genome of this species.

The complex symbiosis of plants root nodules with nitrogen-fixing bacteria enables their survival on nitrogen-poor soils and has a major impact on global nitrogen cycles and food production. It is restricted to a small subset of plant species belonging to four closely related orders of flowering plants, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo) clade. Of the 30 families within this clade, only 10 contain nodulating species and these are phylogenetically scattered throughout the clade. The evolutionary and molecular basis for this scattered distribution has to date remained unclear.
To facilitate comparative phylogenetic analysis covering the FaFaCuRo clade, the genomes of eight nodulating and three closely related non-nodulating plant species have been sequenced and the data is presented here for download.
Whole genome sequencing for the ten newly sequenced genomes was performed using Illumina sequencing technology (HISEQ2000 and HISEQ4000 sequencing technology) at BGI-Shenzhen. Hierarchical library construction strategy was applied utilising multiple pair-end libraries with insert sizes of 170, 250, 350, 500, and 800bp and mate-pair libraries with insert sizes of 2, 5, 10, and 20kb. Most of the paired-end and mate-pair libraries were prepared from large genomic fragments, typically 20-40kb in size or even larger. For more detailed information on the assembly pipeline see the published paper.
Making up this dataset, the legume species selected for this purpose comprise of two non-nodulator species, Nissolia schottii and Cercis canadensis, and two nodulators, Chamaecrista fasciculata and the touch-sensitive Mimosa pudica. Six actinorhizal model species representing the Cucurbitales (Datisca glomerata), Fagales (Alnus glutinosa and Casuarina glauca) and Rosales (Discaria trinervis, Dryas drummondii and Purshia tridentata) were selected alongside one closely related non-nodulator (Begonia fuchsioides, Cucurbitales).
The 10 newly sequenced genomes was combined with 27 already sequenced angiosperm genomes and a phylogenetic analysis on 22 candidate genes was conducted. Here we provide not only the assembly and annotation files of the newly sequenced genomes but also the data files produced in our analysis of them. It is hoped these data will aid in the battle for global food security by elucidating the means to transfer the symbiotic capacity to major crop plants that are currently depending on the application of chemical nitrogen fertilizer.

Alnus glutinosa (A. glutinosa) is a nodulating species belonging to the Fagales order. It is nodulated by Frankia bacteria.Alnus contains about 24 species, has a wide range over all continents except Antarctica, covers broad areas such as volcanic ashes, mountain screes, burned forests and glacier moraines as well as anthropic biotopes such as road sides, dam dykes and mine spoils.DNA was collected from 2 g of young leaves were harvested from a single tree growing on the left bank of Rhone River (France).We sequenced the genome to a depth of approximately 325X.The assembled scaffolds of high quality sequences total 600MB, with the contig and scaffold N50 values of 5kb and 96kb respectively. We identified 43,087 protein-coding genes with a mean length of 1,128kb.