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The twelve polyploids of Christmas

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?

December 20, 2018

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.

1. Hardly hapless, haploid Chlamydomonas reinhardtii

Open quote marks

On the first day of Christmas, my true love gave to me;

Chlamydomonas reinhardtii.

Closing quote marks

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.

Chlamydomonas reinhardtii under the microscope.

Chlamydomonas reinhardtii

2. Dippy diploids

Open quote marks

On the second day of Christmas, my true love gave to me;

two sets of chromosomes, and

Chlamydomonas reinhardtii.

Closing quote marks

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!

Humans have 46 chromosomes (23 pairs) but goldfish have 100 chromosomes!

Goldfish

3. Trippy triploids

Open quote marks

On the third day of Christmas, my true love gave to me;

three seedless watermelons,

two sets of chromosomes, and

Chlamydomonas reinhardtii!

Closing quote marks

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?

Tardigrades and seedless watermelons have three sets of chromosomes.

Tardigrades

4. Tetraploid tetris

Open quote marks

On the fourth day of Christmas, my true love gave to me;

four tagliatelle,

three seedless watermelons,

two sets of chromosomes, and

Chlamydomonas reinhardtii!

Closing quote marks

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.

5. Pentaploids a plenty

Open quote marks

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!

Closing quote marks

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.

Allium ampeloprasum - commonly known as wild leek, a key soup ingredient.

Allium ampeloprasum - wild leek

6. A heck of a lot of hexaploids

Open quote marks

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!

Closing quote marks

Hexaploids are something we’re very familiar with at the Earlham Institute. Not only did we sequence the bread wheat genome properly for the first time, we’ve contributed to each and every improvement of it. With tools such as KAT and MIKADO, our scientists have been hard at work decoding this ridiculously complex genome - as well as finding ways to improve the resilience of cultivated varieties by looking for much needed diversity among its many wild ancestors.

Also hexaploid - the Coast Redwood, Sequoia sempervirens, as well as the Kiwi fruit.

Kiwi fruit is hexaploid.

Kiwi fruit

7. Happy heptaploids

Open quote marks

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!

Closing quote marks

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?

An example of a heptaploid is the Siberian Sturgeon (Acipenser baerii).

Siberian Sturgeon

8. Octoploid occult

Open quote marks

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!

Closing quote marks

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!

9. Nonaploid nonsense

Open quote marks

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!

Closing quote marks

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?!

The Japanese Persimmon tree (Diospyros kaki) is Nonaploid.

Persimmon tree

10. Decaploid decadence

Open quote marks

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!

Closing quote marks

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).

Fragaria x ananassa (strawberry) is always octaploid, but a strawberry can be diploid, tetraploid, hexaploid, octaploid or decaploid (Fragaria iturupensis), making their genomes really complicated to decode.

Strawberries

11. Gimme some sugar! Handy hendecaploids.

Open quote marks

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!

Closing quote marks

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!

12. Toad in the hole! Dandy dodecaploids.

Open quote marks

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!

Closing quote marks

We daresay there are organisms with an even greater number of sets of chromosomes, but pulling nonaploids out of the bag was difficult enough for this article.

We’ll leave you with the Uganda Clawed Frog, which has a whopping twelve sets of chromosomes. Fancy that!

Uganda clawed frog (Xenopus Ruwenzoriensis) which has an amazing twelve sets of chromosomes!

Uganda clawed frog - Xenopus Ruwenzoriensis

All together now...

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!

Season's greetings from the EI communications team!

Article author

Peter Bickerton

Scientific Communications & Outreach Manager