Ho-ho-ho! At Earlham Institute we love a polyploid organism. Why stick to sequencing and decoding boring diploids when you have access to some of the biggest supercomputing power for life science research in Europe?
The twelve days of Christmas has been repeated so often we thought it was time for a change, so here’s a polyploid twist to sing while you peel your spuds, brandy your puds and score your sprouts this Christmas Day morning.
On the first day of Christmas, my true love gave to me;
Chlamydomonas reinhardtii.
Algae are the much underappreciated masters of the Earth, providing up to two thirds of all the oxygen we breathe - so obviously they should be number 1. These tiny green cells (and brown, red, pink, golden) form the basis of the food chain in the oceans and freshwater systems of earth, while pumping out oxygen. They are also found living symbiotically with fungi in lichen, as well as with polyps in coral reefs - leading to the splendid colours we see in spectacular locations such as Australia’s Great Barrier Reef.
The green alga Chlamydomonas reinhardtii lives most of its life as a haploid organism - getting by with one set of perfectly functional chromosomes. Many organisms have a haploid stage - just think of human egg and sperm - but Chlamydomonas live out most of their existence in such a way. Indeed, they only really mate and produce diploid (two sets of chromosomes) cells when conditions require them to shut down - such as when nitrogen becomes exhausted.
Chlamydomonas reinhardtii are generally pretty awesome - they have ridiculously efficient photosynthesis due to the presence of a pyrenoid, and they also have an eyespot equipped with a Channelrhodopsin protein that is a distant ancestor of the rods we have in the human eye. They’re also almost half animal, half plant, and neither of the two, so they’re a treasure trove of evolutionary questions that we’re still unravelling.
The author also did his PhD looking at calcium signalling in Chlamydomonas, so has a soft spot for them.
On the second day of Christmas, my true love gave to me;
two sets of chromosomes, and
Chlamydomonas reinhardtii.
Ok, so diploids are all around us - most mammals have two sets of chromosomes, which makes for some handy genetic reshuffling.
It makes sense, right? One set of chromosomes from the dad, one set from the mum, a bit of mixing and some genetic reshuffling leads to more genetic variation. This is indeed the sexual strategy employed by a great range of organisms.
However, diploid organisms can have vastly differing numbers of overall chromosomes. Humans have a measly 46 (23 pairs) - whereas the tiny goldfish has a staggering 100!
On the third day of Christmas, my true love gave to me;
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
What sort of organisms have three sets of chromosomes?
TARDIGRADES! And seedless watermelons. Triploidy would often render many organisms infertile, which is actually quite handy when you want to produce seedless fruit. Of course, cultivating it then becomes a different challenge - the seeds are generated from cross-breeding diploid and tetraploid (4 sets of chromosomes) plants - but you have happy consumers who don’t spend half their day spitting out seeds.
Tardigrades, though. The ultimate organism. Radiation, heat, outer space - who cares when you’re a tardigrade?
On the fourth day of Christmas, my true love gave to me;
four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
Sequencing organisms gets a bit more difficult the more chromosome pairs you have - especially when you’ve got four versions of the same gene!
Durum wheat is an organism we’ve tackled at Earlham Institute, which has a tetraploid genome due to the hybridisation of two wild grass species. Durum wheat is the second most widely cultivated variety of wheat - and gives Italy its pasta.
On the fifth day of Christmas, my true love gave to me;
five wild leek rings,
four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
It might sound unlikely, but pentaploid organisms do indeed exist - many of them among the members of the onion family. Allium ampeloprasum, for example, the wild leek, has five sets of chromosomes and gets on just fine.
Indeed, one of the cultivated forms is leek - the national plant of Wales and invaluable constituent of a leek and potato soup.
On the sixth day of Christmas, my true love gave to me;
six wheat ears a swaying,
five wild leek rings,
four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
It might sound unlikely, but pentaploid organisms do indeed exist - many of them among the members of the onion family. Allium ampeloprasum, for example, the wild leek, has five sets of chromosomes and gets on just fine.
Indeed, one of the cultivated forms is leek - the national plant of Wales and invaluable constituent of a leek and potato soup.
On the seventh day of Christmas, my true love gave to me;
seven sturgeon swimming,
six wheat ears a swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
Though rare, it’s possible to find heptaploid eggs among the progeny of certain triploid amphibian species after going through temperature shock.
Perhaps this temperature shock is also the reason that some Siberian Sturgeon have also been known to have seven sets of chromosomes?
On the eighth day of Christmas, my true love gave to me;
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
There are loads of octoploids, another type of sturgeon among them. Apparently sturgeons love the complexity and diversity that comes with juggling duplicate genes.
Another among the octoploids is the Dahlia, transposon-rich flowers of the Asteraceae. No wonder they have such a dazzling array of forms with all those genes jumping between so many pairs of chromosomes!
On the ninth day of Christmas, my true love gave to me;
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears a swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
Believe it or not, it’s possible to have nine sets of chromosomes. Indeed, one such organism is Brachiaria humidicola, a type of grass native to African swamps.
It has potential as a forage crop for grazing animals on marginal land. Some people have also made some nonaploid Japanese Persimmons - why on earth not?!
On the tenth day of Christmas, my true love gave to me;
ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears a swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
You’ll never look at a strawberry the same again, but they have an abundance of duplicated chromosomes. Ok, the original woodland variety was diploid - but now the cultivated varieties can be tetraploid, hexaploid, octaploid or decaploid!
So many, in fact, that the Clavijo group at EI is determined to unravel their complicated genomes (though they worked on the octoploid strawberry).
On the eleventh day of Christmas, my true love gave to me;
eleven piping icing,
ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
A type of sugarcane, Saccharum spontaneum, has varying numbers of chromosome sets representing an abundance of potential diversity that we can introduce into more commonly cultivated varieties of sugarcane.
Just imagine the possibilities!
On the twelfth day of Christmas, my true love gave to me;
twelve clawed frogs clawing,
eleven piping icing,
ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears a swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
A type of sugarcane, Saccharum spontaneum, has varying numbers of chromosome sets representing an abundance of potential diversity that we can introduce into more commonly cultivated varieties of sugarcane.
Just imagine the possibilities!
On the first day of Christmas, my true love gave to me;
Chlamydomonas reinhardtii!
On the second day of Christmas, my true love gave to me;
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the third day of Christmas, my true love gave to me;
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the fourth day of Christmas, my true love gave to me;
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the fifth day of Christmas, my true love gave to me;
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the sixth day of Christmas, my true love gave to me;
Six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the seventh day of Christmas, my true love gave to me;
Seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the eighth day of Christmas, my true love gave to me;
Eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the ninth day of Christmas, my true love gave to me;
Nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the tenth day of Christmas, my true love gave to me;
Ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the eleventh day of Christmas, my true love gave to me;
Eleven piping icing,
ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
On the twelfth day of Christmas, my true love gave to me;
Twelve clawed frogs clawing,
eleven piping icing,
ten strawberries steeping,
nine swampy grasses,
eight Dahlia dancing,
seven sturgeon swimming,
six wheat ears swaying,
five wild leek rings.
Four tagliatelle,
three seedless watermelons,
two sets of chromosomes, and
Chlamydomonas reinhardtii!
