Putative phytological pugilism (probably…) [or, One species – two genomes?]

In the genteel world of botany, one may be surprised to discover that – occasionally! – disagreements can arise, and that tempers can get just a little heated. Well, in an attempt to expose the darker side to the otherwise seemingly tranquil and sweetness-and-light domain of plant biology – and incidentally to show what the ‘-phyte’ suffix really means! – I offer the following cautionary tale. When a species’ genome – draft or otherwise – is published, you assume that to be definitive. But in the case of pigeon pea (Cajanus cajan – ‘an orphan legume crop of resource-poor farmers’) it seems that this may not be the case.

I was interested to note that a draft of the pigeon pea genome had been published by Rajeev Varshney and co-workers (Nature Biotechnology). And reading that the report ‘presents the genome of the first orphan legume crop and the second food legume (after soybean)’, I was happy to leave it at that. However, noting that C. cajan ‘plays a substantial role in the livelihood of resource-poor smallholder farmers in marginal environments’, I was keen to find out more about this crop plant and duly consulted the oracle – aka Wikipedia (I can anticipate/sense your communal shudder as I write/you read those words, but I’m allowed to do this – see ‘Embrace Wikipedia!(?)’). Well, I certainly found more than I was expecting, including this gem, ‘The first draft of pigeon pea genome sequence was done by a group of 31 Indian scientists from the Indian Council of Agricultural Research under the leadership of Nagendra Kumar Singh. The paper is published in one of the Indian journal’ [sic]. I don’t know who contributed to the Wikipedia entry, but I tracked down the article referred to – by Nagendra K. Singh et al. (Journal of Plant Biochemistry and Biotechnology), and entitled, ‘The first draft of the pigeonpea genome sequence’. Interestingly, both papers sequenced pigeon pea variety ‘Asha’, but Singh et al.’s was received by the journal on 2nd July 2011, whereas Varshney et al.’s wasn’t received until… 19th July 2011. (Interestingly, Singh et al.’s paper wasn’t cited by Varshney et al. – but you wouldn’t necessarily expect it to be since both manuscripts were received within a few days of each other…). But, as Varshney et al. opine, ‘This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries’. So, whatever the ins-and-outs or rights-and-wrongs of this incident – and we must surely recognise that this has ‘put the cat amongst the “pigeons”’ – isn’t it good that we have such a great genomic resource for this crop plant (that I suspect many of us had probably not heard much about before)? Surely, we can all agree on that?

Well, maybe not. Ultimately, and regardless of who achieved this feat first, how close are the two published genomes? Are they the same? If not, is one more ‘correct’ than the other? Which one should be used to do further work with this important legume, known as ‘the poor man’s meat’?