Tag Archives: Monocots

Orchid Symbioses Symposium and Workshop, Spring 2013

Those that know me know that I’ve got a thing for orchids.  From my point of view, what’s not to like: they have exceptionally diverse morphology, have complicated natural histories, have equally diverse interactions with pollinating insects, and – most important for me – are obligate mycorrhizal formers with a wide array of fungal symbionts.  I’m quite surprised we don’t have more scientists studying them.

The journal New Phytologist has already sponsored 30 symposia on plant biology – the 31st symposium has been announced and will be focused on orchids and their interactions with mycorrhizal fungi and insects.  The goal of this meeting will be to bring together scientists studying orchids and advance the study of orchids and their symbiotic fungi and co-evolved insects.  As someone who has attended in the past, I cannot place enough emphasis on how rewarding these New Phytologist symposia have been to me.  There is plenty of time to register and apply for a travel grant.

This particular symposium will be held in conjunction with the 5th International Orchid Workshop this upcoming spring.  Both meetings will be held back to back at very close locales in Italy.

Genome Sequence of the Date Palm

Published in the June 2011 issue of the journal Nature Biotechnology was a paper reporting on the genome sequence of the data palm, Phoenix dactylifera.  This paper, authored by Al-Dous et al., addressed the genome sequencing and de novo assembly of this agriculturally important monocot tree, along with comparative genomics with other plants.

Dates have been found in the tombs of pharaohs estimated at 8,000 years old.  Fields of agriculturally planted trees, estimated to be older than 5,000 years, suggest the date palm is one of the oldest cultivated plants in the world.  Dates are the most important agricultural crop in the hot and arid regions surrounding the Arabian Gulf and their global production is close to 7 million tons yearly.

Despite a prolonged emphasis on their agriculture, there are a few problems to deal with if you are a date grower.  Typical of tree crops, there is a long generation time from seedling to fruit harvesting.  Additionally, only the female date palm provides fruit and it takes at least 5 years after seed germination to tell if you have a male or female plant.  To make it even harder for a date grower, there are more than 2000 date varieties, each exhibiting its own color, flavor, size, shape, and ripening schedule, and they are all really hard to keep track of based on conventional techniques.

In an effort to provide genetic resources for date growers and breeders, the authors of this study – who were mainly located in Qutar – sequenced and assembled 380 Mb of the estimated 658 Mb genome of the Khalas cultivar, which is known for high fruit quality.  Generated using short reads from the Illumina Genome Analyzer IIx platform, this partial sequence excluded numerous large repeated regions, includes a predicted 28,890 genes, and represented 18 pairs of chromosomes.  The authors estimate that this draft genome represents roughly 90% of the total genes and 60% of the total genome.

This genome resource also serves a comparative genomics purpose by being the first member of the widespread monocot order Arecales.  To this date, the only Monocots with sequenced genomes – for example: Corn, Rice, and Sorghum – have all been in the grass order, the Poales.

This report is missing some vital information: in addition to an incomplete genome assembly, there is no metabolic, developmental, or gene network pathway reconstruction for the date palm provided in this paper (and unfortunately this paper also includes some glaring typos in the citation section).  In place of these expected analyses, the authors conducted a throughout survey of SNPs in this Khalas cultivar, along with eight additional cultivars common in breeding programs for the date palm.  Within these nine cultivars, 3,518,029 SNPs were determined, but quite interestingly, a total of 32 SNPs could be used to differentiate the cultivars.

In addition to the throughout SNP analysis, the researchers then did a full parentage analysis of the cultivars used in this study, which includes the famous date varieties such as Deglet Noor, Dayri, and Medjool.  Here‘s an article in Nature Middle East on the importance of understanding this parentage and gender analysis.

Although this is a draft genome still being completed and undergoing resequencing, namely the tools provided by the authors, the SNP and parentage analysis, should provide date palm breeders with many resources for improved fruit quality and this genome represents an exciting piece of the monocot evolutionary puzzle.