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Table 1 Progress of African Orphan Crop Consortium (AOCC) for three major activities in genomics workflow

From: African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

Sl#Species name (growth habit/type of crop)Common name and distribution in AfricaWhole genome sequencing status (WGS)Transcriptome sequencing statusRe-sequencing status
1Faidherbia albida (T-Fr)Apple ring acacia, distributed throughout the dry zones of Africa, predominantly in the east and southern Africa (Orwa et al. 2009), is an important agroforestry species for land restoration (PROTA 2018)Published, Chang et al. (2018a, b)RNA sequencedIn the pipeline
2Vigna subterranea (A-OS)Bambara groundnut originated in western Africa and grown for seeds in sub-Saharan semi-arid tropical regions of Nigeria, Cameroon and eastern Africa (Tanzania, Uganda) (PROTA 2018)Published, Chang et al. (2018a, c)RNA sequencedPartially done
3Lablab purpureus (A-LS)Hyacinth bean is consumed as a vegetable in tropical Africa (Nigeria and Kenya, Rwanda, and Ethiopia) (PROTA 2018)Published, Chang et al. (2018a, d)RNA sequencedPartially done
4Sclerocarya birrea (T-Fr)Marula tree occurs throughout sub-Saharan Africa except the humid zones. A wine called Amarula is commercially made from fruits in southern Africa (PROTA 2018)Published, Chang et al. (2018a, e)RNA sequencedIn the pipeline
5Moringa oleifera (T-LFV)Drumstick, Indian in origin but now naturalized in Africa and found throughout tropics and subtropics of Africa (PROTA 2018), is used as a leafy and fruit vegetablePublished, Chang et al. (2018a, f)RNA sequencedPartially done
6Solanum aethiopicum (A-LV)African eggplant is found across the tropical sub-Saharan Africa, especially western, central, and some parts of eastern Africa (Uganda) Schippers (2000; Maundu et al. 2009), consumed as a leafy vegetablePublished, Song et al. (2019)RNA sequencedYet to begin
7Digitaria exilis (A-G)Fonio, consumed in the form of grains, is cultivated in western Africa since ancient time and now is grown scattered across the same region (PROTA 2018)Final assemblyYet to beginYet to begin
8Eleusine coracana (A-G)Finger millet, an African-origin cereal, is found to be growing in all the semi-arid and arid tropics of Africa in eastern, western, and southern regions (USDA 2019). Grains are consumed in the form of flour or fermented to make edible drinkFinal assemblyRNA sequencedPartially done
9Gynandropsis gynandra (A-LV)Spider plant is generally found distributed all over the Africa near agricultural land and human settlements, but grown in drier zones of southern Africa in South Africa, Zimbabwe etc. (PROTA 2018), and is consumed as a leafy vegetableFinal assemblyIn the pipelinePartially done
10Annona cherimola (T-Fr)Cherimoya, a fruit tree, also referred to as custard apple is grown in tropical Africa specifically in western Africa (Algeria, Egypt, Libya, Somalia, and South Africa) (USDA 2019)Final assemblyIn the pipelineYet to begin
11Artocarpus heterophyllus (T-Fr)Jackfruit is originally from Southeast Asia (India), and now naturalized in Africa and found to be growing in western and south-western Africa (Orwa et al. 2009)Final assemblyIn the pipelineYet to begin
12Artocarpus altilis (T-Fr)Bread fruit is a naturalized widely found across Africa, mainly in tropical sub-Saharan Africa (CABI 2018)Final assemblyIn the pipelineYet to begin
13Celosia argentea (A-LV)Cockscomb is used as a leafy vegetable and medicinal plant in Kenya, Congo, Benin, and Ethiopia, grown on scattered plots in home gardens and priced during dry seasons (PROTA 2018)Data generation onIn the pipelineYet to begin
14Phaseolus vulgaris (A-LV, FV)Common bean is widely grown all over Africa with the main countries being Burundi, Kenya, Rwanda, DR Congo, Tanzania, Uganda, and Sudan (Wortmann et al. 1998). The green pods and young or dried seeds are consumed as foodData generation onYet to beginIn the pipeline
15Solanum nigrum (A-LV)Black or African nightshade is consumed as fruits or leaves. There is no exact information about its distribution (PROTA 2018), but found in tropical sub-Saharan regions of Africa (USDA 2019)Data generation onIn the pipelineYet to begin
16Adansonia digitata (T-LV, F)Baobab occurs naturally all over the sub-Saharan Africa. Fruits and leaves are consumed in various parts of Africa. Except for a few countries in central Africa (Rwanda, Burundi, Djibouti, and Uganda), it is found all over sub-Saharan Africa (PROTA 2018)Data generation onTissue collectedIn the pipeline
17Anacardium occidentale (T-Fr)Cashew nut is found and grown in coastal and humid countries in eastern Africa (Kenya, Mozambique, Gambia, Sudan, Tanzania, Uganda) (Orwa et al. 2009)Data generation onIn the pipelineYet to begin
18Dovyalis caffra (T-Fr)Kei apple or wild apricot is a fruit tree found in southern Africa (South Africa, Botswana, Namibia, Lesotho, Malawi, Mozambique, South Africa, Swaziland, Zimbabwe) and introduced in Ethiopia, Kenya, Sudan, Tanzania, and Uganda (Orwa et al. 2009)Data generation onIn the pipelineYet to begin
19Parinari curatellifolia (T-Fr)Mbola plum, found in almost all the sub-Saharan Africa (Orwa et al. 2009), is grown for fruitsData generation onYet to beginIn the pipeline
20Parkia biglobosa (T-Fr)Monkey cutlass tree or African locust bean produces edible fruits and seeds the tree is a native of western Africa and found distributed across central and eastern Africa (Orwa et al. 2009; PROTA 2018)Data generation onIn the pipelineYet to begin
21Saba senegalensis (WCL-Fr)Saba produces edible fruits and is found in western Africa and eastern-most Africa (Orwa et al. 2009)Data generation onYet to beginYet to begin
22Uapaca kirkiana (T-Fr)Wild loquat is a native fruit species of southern Africa (Angola, DR Congo, Malawi, Mozambique, Tanzania, Zambia, and Zimbabwe (Orwa et al. 2009))Data generation onIn the pipelineIn the pipeline
23Vitellaria paradoxa (T-Fr, OS)Shea butter tree is a native of western Africa, but found across sub-Saharan belt till Sudan and Ethiopia (Orwa et al. 2009). Kernels, seed oil, and pulp are consumed by locals and seed oil is widely used in cosmetic and confectionary industryData generation onIn the pipelineIn the pipeline
24Casimiroa edulis (T-Fr)White sapote is a fruit tree widely found in Tanzania and South Africa (Orwa et al. 2009)Data generation onIn the pipelineYet to begin
25Dacryodes edulis (T-Fr)African plum or Safou is a native fruit species of western Africa, but also distributed in central Africa (Orwa et al. 2009). Fruits are eaten raw or after boiling or roastingData generation onIn the pipelineYet to begin
26Ziziphus mauritiana (T-Fr)Jujube is a fruit species naturalized in Africa which is grown in western, central, and eastern Africa (Orwa et al. 2009)Data generation onIn the pipelineYet to begin
27Tamarindus indica (T-Fr)Tamarind, found across sub-Saharan western, central, and eastern Africa (Orwa et al. 2009), produces edible sour fruit which is used as a part of culinary preparations or consumed as juiceData generation onTissue collectedYet to begin
28Syzygium guineense (T)Water berry is a fruit tree found in its native range of eastern and southern Africa (Orwa et al. 2009)Data generation onTissue collectedYet to begin
29Irvingia gabonensis (T)African bush mango is a native fruit species of western Africa and is found distributed across central and eastern sub-Saharan Africa till Uganda and Sudan (Orwa et al. 2009). Fruits can be eaten raw, but some tree parts are also used in the local dye industryData generation onYet to beginYet to begin
30Ricinodendron heudelotii (T-Fr, Sp)Groundnut tree is a native tree of western Africa and found distributed across central and eastern sub-Saharan Africa (Orwa et al. 2009). The fruits are edible and after drying are used a spiceData generation onTissue collectedYet to begin
31Detarium microcarpum (T-Fr)Sweet dattock occurs in the drier regions of west and central Africa (PROTA 2018). The fruit can be eaten raw or fruit pulp can be dried and storedData generation onYet to beginYet to begin
32Garcinia livingstonei (T-Fr)Wild mangosteen is a fruit tree found across southern and eastern Africa (Orwa et al. 2009)Data generation onYet to beginYet to begin
33Dioscorea alata (TDd) (PT-T)Water yam is an introduced tuberous root vegetable crop naturalized in Africa. It is primarily grown predominantly in western Africa (Obidiegwu et al. 2009)Data generation onBy collaboratorIn the pipeline
34Macrotyloma geocarpum (A-PS)Kersting’s groundnut is a pulse crop with similar growth habit as peanut. The seeds are consumed after cooking or roasting and can be made into flour for various uses. It is suggested to have originated from Western Africa and grown as a minor crop in West African Savanna zone, Cameroon, Tchad, and also reported to be grown in Mauritius, Tanzania, and Fizi (Ayenan and Ezin 2016)Yet to beginYet to beginIn the pipeline
35Strychnos cocculoides (T-Fr)Monkey orange, a native fruit tree of southern Africa, is also found in Botswana, Kenya, South Africa, Tanzania, Uganda, Zambia, and Zimbabwe (Orwa et al. 2009)Yet to beginIn the pipelineIn the pipeline
36Strychnos spinosa (T-Fr)Kaffir orange is mainly found in eastern Africa (Kenya Ethiopia, Sudan, Tanzania, Uganda) and Mali, Zambia, and Madagascar (Orwa et al. 2009), which is eaten as raw fruitYet to beginTissue collectedYet to begin
37Vitex doniana (T-Fr)Black plum is predominantly distributed across east and south Africa (Orwa et al. 2009). The fruits are consumed raw or after boilingYet to beginTissue collectedYet to begin
38Allanblackia stuhlmannii (T-Fr, OS)Allanblackia is a native tree of Tanzania and found only in the humid tropical regions of the country (Orwa et al. 2009). The edible seed oil is in high demand locally and internationally and is used in cosmetics and confectionary industryYet to beginTissue collectedYet to begin
39Annona reticulata (T-Fr)Bullock’s heart, a naturalized fruit species in Africa from central America, is predominantly grown in South Africa and sporadically in other tropical African countries (Orwa et al. 2009)Yet to beginTissue collectedYet to begin
40Vangueria madagascariensis (T-Fr)Wild medlar, a fruit tree, is found in east, southern, and southwest Africa (Orwa et al. 2009)Yet to beginIn the pipelineYet to begin
41Passiflora edulis (WCL-Fr)Passion fruit is naturalized fruit species found in sub-Saharan Africa and in grown in eastern and southern African countries (USDA 2019)Yet to beginIn the pipelineYet to begin
42Brassica carinata (A- LV)Ethiopian kale is cultivated in Ethiopia since thousands of years, and also grown in east and southern Africa to some extent (PROTA 2018)By collaboratorIn the pipeline
44Dioscorea rotundata (PT-T)White yam probably originated in west Africa, where it is extensively cultivated (Aighewi et al. 2015)By collaboratorIn the pipeline
45Lens culinaris (A-LS)Lentils are grown in tropical parts of Africa, predominantly in eastern and southern Africa (PROTA 2018)By collaboratorIn the pipeline
46Musa acuminata (NWF-Fr)Musa acuminata is sequenced as one of the parents of widely cultivated triploid banana.Other groupIn the pipeline
47Allium cepa (A-RV)Onion is an introduced root (bulb) vegetable species to Africa and is grown across tropical west, east, and southern Africa (PROTA 2018)By collaboratorYet to begin
48Amaranthus tricolor (A-G)Amaranth species consumed as leafy vegetable, is introduced from tropical Asia, but is now naturalized in Africa and grown in west, east and southern Africa (PROTA 2018)By collaboratorYet to begin
49Carica papaya (P-Fr)Called as Papaya or paw paw in Africa, it is grown for its fruit in east and southern Africa as fruit crop (da Silva et al. 2007)By collaboratorYet to begin
50Citrullus lanatus (A-Fr, OS)Referred to as egusi melon or west African melon, the fruit species originated from western Kalahari region of Namibia and Botswana. Apart from southern Africa, now it is also found across Mediterranean Africa (PROTA 2018)By collaboratorYet to begin
51Cucurbita maxima (A-FV)Pumpkin has been reported from many countries in tropical Africa and probably occurs in all the countries (PROTA 2018), where it is grown as a fruit vegetableDone by CuGenDB; http://cucurbitgenomics.org (Zheng et al. 2019)Yet to begin
52Eragrostis tef (A-G)Tef originated in northern Ethiopia. It is cultivated for its grains and cultivation is confined mainly to Eritrea and Ethiopia (PROTA 2018)By collaboratorYet to begin
53Ipomoea batatas (PR-RV)Sweet potato is an introduced root tuber species to Africa, but now it is grown extensively in all the tropical Africa primarily in eastern and western Africa (Glato et al. 2017)By collaboratorYet to begin
54Musa acuminata AAA Group (Matoke) (NWF-Fr)East African highland bananas or matoke originated in African great lakes region, is eaten as fruit vegetable in Uganda, Tanzania, Burundi, Democratic Republic of Congo, Kenya, and Rwanda (PROMUSA 2017)By collaboratorYet to begin
55Momordica charantia (A-FV)Bitter gourd, a fruit vegetable probably domesticated in India and southern China, occurs almost throughout tropical Africa and occasionally cultivated in east Africa (PROTA 2018)By collaboratorYet to begin
56Mangifera indica (T-Fr)Mango is a naturalized fruit tree in Africa and is grown in tropical parts of Western, and eastern Africa (Orwa et al. 2009)By collaboratorYet to begin
57Macadamia ternifolia (T-Fr)Macadamia nut is an introduced nut tree species grown in Ethiopia, Kenya, Malawi, South Africa, Tanzania, Zimbabwe (Orwa et al. 2009)By collaboratorYet to begin
58Persea americana (T-Fr)Avocado is an introduced fruit tree in Africa, which is grown almost all over sub-Saharan Africa (Orwa et al. 2009)By collaboratorYet to begin
59Psidium guajava (T-Fr)Guava, a naturalized fruit tree grown in Ethiopia, South Africa, Uganda, Togo, Senegal, and Nigeria (Orwa et al. 2009)Other groupYet to begin
60Morus alba (T-LV, FV)Mulberry is grown in eastern and southern Africa (Orwa et al. 2009), where the fruit is consumed fresh or as juiceOther groupYet to begin
  1. Growth habit depicted as: A annual, T tree, PT perennial tuber, WCL woody climber or liana, NWF non-woody fruit, PR perennial root. Economic part depicted as: Fr fruit, FV fruit vegetable, LV leafy vegetable, RV root vegetable, G grains, T tuber, OS oil seed, Sp spice’, PS pulse seed. As soon as the DNA/RNA enters into the specific activity, it gets logged as “in the pipeline”. For 18 species, the WGS and transcriptome sequencing is being done either by one of the AOCC’s collaborators or other groups. The information about “Other group” and “By collaborator” is still being worked out and thus is not final