Uncovering the genome sequence of the water yam orphan crop

Yams (genus Dioscorea) are an important source of food and income for millions of smallholder farmers in the tropical and subtropical regions of Africa, Asia, the Pacific and Latin America. Water yam (Dioscorea alata) is the most widely distributed cultivated yam species in the world. It is superior to most cultivated yam species due to its potential to yield under low to average soil fertility and its high nutritional quality. However, it is susceptible to disease and its complex genome, long growth cycle and erratic flowering make conventional breeding for desired traits difficult.

Like many other crops crucial to sustainable development, yams are poorly characterised and referred to as “neglected” or “orphan” crops. However, new efforts to redress this imbalance are in progress. One organisation co-ordinating this activity is the African Orphan Crops Consortium (africanorphancrops.org) which aims to characterise 101 orphan crops indigenous to Africa and selected by African crop breeders.

The Dundee team got involved in the water yam project because of their expertise in sequencing RNA. When the genes encoded in DNA are switched on, they are copied into a related molecule called RNA. As a result, sequencing RNA helps to reveal what the genome encodes. However, since the RNA can be altered in many different ways this is not entirely straightforward. In addition, RNA is typically sequenced by copying it back into DNA and fragmenting it into small pieces to accommodate current sequencing technologies. These steps, can make the correct interpretation of the original RNA molecules very difficult.

The Dundee team have pioneered the application of a new technology to sequence RNA called Nanopore Direct RNA Sequencing. Their ground-breaking study on adapting this technology was recently published in the scientific journal eLIFE. In this approach RNA is passed directly though nanopores to reveal the sequence of full-length RNA molecules.

The scientists in Dundee sequenced water yam RNA provided by the African Orphan Crops Consortium based in Nairobi, Kenya. By combining the data with the DNA sequence information and RNA sequence information obtained by conventional technologies, the Dundee team could improve the annotation and understanding, of what the water yam genome encodes. For example, they could clearly distinguish where genes end and on which strand of DNA they were encoded.

The Dundee team was led by Professors Gordon Simpson and Geoff Barton, with computational analysis by Dr Matt Parker and RNA analysis by Dr Kasia Knop. Professor Simpson also holds a position at The James Hutton Institute.

Commenting on the study, Professor Simpson said, “The major part of this programme was the sequencing of the yam genomic DNA, but our work with nanopore direct RNA sequencing helped to clarify what the genome encodes. This was one of our first applications of this new sequencing technology, and we have made a number of improvements to how we sequence the RNA and how we analyse the data since then.

We continue to work with the AOCC to sequence other orphan crops and we are collaborating with scientists at The International Institute of Tropical Agriculture, Nigeria, to understand the erratic flowering behaviour of yams that hinders successful breeding programmes.

Modern agriculture is dominated by a handful of intensely researched crops, but to diversify global food supply, enhance agricultural productivity and tackle malnutrition there is a need to focus on neglected crops utilized in rural societies that have received little attention for crop improvement. In this sense, I feel this is some of the most important work taking place in my lab.”

The water yam genome project was supported by a US National Sciences Foundation-Gates Foundation grant to scientists at the University of California, Berkeley, The International Institute of Tropical Agriculture and The National Root Crops Research Institute in Nigeria. 

The Dundee team were funded by GCRF (Global Challenges Research Fund). Kasia Knop was funded by a Marie-Sklodowska Curie Fellowship from the European Commission.

The water yam genome is freely available with the release notes on the Dundee team’s contribution to the annotation here: https://phytozome-next.jgi.doe.gov/info/Dalata_v2_1