Olive Threat, Ginkgo Genome

Something’s killing Europe’s olive trees: a bacterium that’s probably spread by insects. Scientists don’t know how to stop the disease, not yet.

Other scientists analyzed the Ginkgo genome. What they found helps explain the tree’s remarkable endurance.

1. Olive Quick Decline Syndrome
   • One Bacterium, Lots of Plant Diseases
2. Decoding the Ginkgo Genome
   • Ginkgos, Ginkgoales, and a Lightly-Nibbled Leaf
   • Ginkgo Biloba: Near-Legendary Durability
   • A Huge Genome

Truth and Tiglath-Pileser III

If this is your first time here, I may have some explaining to do.

I’m a Christian, a Catholic, and take my faith and our Lord very seriously. That’s not even close to insisting that we knew everything there was to know about the cosmos back when Tiglath-Pileser III ruled Assyria.

My faith emphatically does not depend on rejecting what we’re learning about this wonder-filled universe.

Truth is beautiful, and is important. It can be expressed in words, “the rational expression of the knowledge of created and uncreated reality;” in “the order and harmony of the cosmos;” or in other ways. (Catechism of the Catholic Church, 2500)

We can learn a bit about God by noticing “the world’s order and beauty,” which reflects God’s infinite beauty. (Catechism, 31–32, 341)

We’re made “in the image of God,” with a thirst for truth and God. Observing the world’s order and beauty, studying how things work, helps us learn about God. (Genesis 1:26, 2:7; Catechism, 27, 31–35, 282–289, 355–361)

Science and technology, studying the universe and using what we learn, is part of being human. (Catechism, 2292–2296)

I’ve been over that before. (October 28, 2016)

“Whatever God Wills is Done”

We’re learning that this universe is vast, ancient, and has been changing ever since it started, several billion years back. I see these scientific discoveries as invitations “to even greater admiration for the greatness of the Creator.” (Catechism, 283)

Even if I didn’t approve of the reality we’re in, it wouldn’t matter much:

“Our God is in heaven; whatever God wills is done.”
(Psalms 115:3)

And I’m okay with that.

1. Olive Quick Decline Syndrome

(From EPPO, via BBC News, used w/o permission.)
(“The invasive pathogen has affected thousands of hectares of olive plantations in Puglia, southern Italy”

“Olive killer disease arrives on Mallorca”
Mark Kinver, BBC News (November 21, 2016)

“A disease that poses a ‘very serious threat’ to the EU’s olive industry has been recorded on the Spanish island of Mallorca for the first time.

“Island officials said a movement ban covering 15,000 hectares had been imposed and measures had been taken to ‘contain and eradicate its spread’.

“Experts describe Xylella fastidiosa as one of the ‘most dangerous pathogens worldwide’.

“It was first recorded in the EU in 2013, and has since spread westwards….”

The article doesn’t say who the “experts” are. My guess is that Xylella fastidiosa got labeled “most dangerous” because the bacterium can infect several important crops.

The disease is called phoney peach disease, bacterial leaf scorch, and oleander leaf scorch: depending on what plants got sick, and where they are. Also Pierce’s disease, citrus variegated chlorosis disease, and olive quick decline syndrome. (Wikipedia)

X. fastidiosa diseases here in the Americas get spread by insects like the glassy-winged sharpshooter and other leafhoppers. Sucking insects probably spread it in Europe, too, but researchers are still working on details.¹

Mark Kinver’s article says the European Union makes and consumes most of the world’s olive oil. This disease probably pushed olive oil prices up by 20% in 2015.

My guess is that it’s hurting households as well as olive oil producers and distributors.

One Bacterium, Lots of Plant Diseases

Pierce’s disease, an X. fastidiosa disease, became a problem for the California wine industry in the 1990s, when glassy-winged sharpshooters showed up in the Temecula Valley.

Scientists still haven’t found a cure or control method, but they’ve been learning a lot about how the disease spreads: and the bacterium’s genes.

At least 83 of X. fastidiosa’s genes come from bacteriophage. Some of them make the bacterium more virulent. I think that’s not entirely bad news, though.

Knowing how the bacterium works on the sub-cellular level may help scientists develop disease-resistant crops. I’ve talked about horizontal gene transfer and genetic engineering before.² (October 7, 2016; July 22, 2016)

2. Decoding the Ginkgo Genome

(From Thinkstock, via BBC News, used w/o permission.)

“Ginkgo ‘living fossil’ genome decoded”
BBC News (November 21, 2016)

“The Ginkgo tree has had its genetic code laid bare by researchers.

“The tree is famed for being a ‘living fossil’ – a term used to describe those organisms that have experienced very little change over millions of years.

“In the case of the Ginkgo, there are specimens preserved in the rock record from 270 million years ago, in the Permian Period.

“The Chinese-led research team says the new information should help to explain the tree’s evolutionary success….”

Back in the ‘good old days,’ this sort of research would be passed around a select group of professors and student assistants, plus whoever had the money and qualifications to get access to academic journals. As I keep saying, I don’t miss the ‘good old days.’

The research team’s results are available online, under Creative Commons Attribution 4.0 International License, so anyone who’s interested can see what they learned:

• “Draft genome of the living fossil Ginkgo biloba”
  Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu, Song Ge, Wenbin Chen; GigaScience, BioMed Central (received August 17, 2016; accepted November 1, 2016; published November 21, 2016)

Ginkgos, Ginkgoales, and a Lightly-Nibbled Leaf

The BBC News article’s picture of a contemporary ginkgo leaf superimposed on a fossilized one is impressive, although the fossil seems to be the lightly-nibbled 6.7 cm tall Ginkgo biloba leaf found in the Klondike Mountain Formation.

That leaf fell about 49,000,000 years back, and was in the Stonerose Interpretive Center Collection in 2008.

Ginkgo biloba is the only species of Ginkgo around these days. It’s the only survivor of the Ginkgo genus. The genus first showed up in the Early Jurassic, 180,000,000 years back; give or take ten million.

The Ginkgo genus is part of the Ginkgoales order; and that’s what goes back to the Permian, about 270,000,000 years ago.

Genus is the taxonomic rank between species and family.

We’ve fine-tuned taxonomy quite a bit since Carl Linnaeus set up the basics in 1735.

I’ve mentioned him before; also Anaximander, Aristotle, and the florid prose of Thomas Hawkins; none of which is something you need to remember. (October 28, 2016; September 23, 2016)

I’ve had a hard time finding a generally-accepted age for the Ginkgo biloba species. Part of the trouble, I suspect, is that what we do know about G. biloba is — odd.

For one thing, Ginkgo biloba is almost identical to Ginkgo adiantoides; a tree that lived in the Late Cretaceous to the Miocene. That’s about 80,000,000 to 23,000,000 years back. Some critters have been remarkably stable over the ages: but that’s a long time.³

Ginkgo Biloba: Near-Legendary Durability

(From Hitachi-Train, Urashimataro, via Wikimedia Commons, used w/o permission.)
(Tsurugaoka Hachimangū shrine’s thousand-year-old ginkgo, after a March, 2010 storm.)

The ginkgo genus has been declining since the early Cretaceous, some 145,000,000 years back. Like I said, these days it’s down to one species, native to part of China. Oddly enough, Ginkgo biloba apparently isn’t an endangered species.

That’s probably because humans have been planting the trees across Eurasia and, more recently, the Americas. It helps that G. biloba doesn’t mind pollution or confined patches of soil, and resists many diseases.

Ginkgo biloba earned a near-legendary reputation for durability after August 6, 1945, when a half-dozen Ginikgos were among the hibakujumoku, 被爆樹木, in Hiroshima. The trees were scorched, but are still growing there.

Another ginkgo had been growing near a stairway at the Tsurugaoka Hachimangū Shrine, 鶴岡八幡宮, for about a thousand years ‐ until a pre-dawn storm in March, 2010.

An expert said the tree was done for, so folks kept the stump and replanted part of the trunk. Both were sprouting leaves in July of that year.

I can understand folks liking trees. I’ve talked about Christmas trees, Donar’s Oak, deodar and Nang Tani before, and that’s another topic. (July 24, 2016)

A Huge Genome

The Ginkgo biloba genome is huge, with 41,840 annotated genes. The G. biloba’s genome is ‘written’ with 10,600,000,000 DNA ‘letters,’ compared to the human genome’s roughly 3,000,000,000.

Quite a bit of that’s multiple redundancy. As the research team put it:

“…Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent….”
(“Draft genome of the living fossil Ginkgo biloba,” Wenbin Chen et. al. (November 21, 2016))

The scientists say that massive accumulation of genetic code “…indicates a remarkable array of chemical and antibacterial defense

“…Its anti-insect arsenal is particularly smart. The Ginkgo will synthesise one set of chemicals to directly fight a pest, but also release another set of compounds that specifically attract the insect’s enemies….”
(BBC News)

No wonder G. biloba has been so durable. It’s got a vast instruction manual for handling assorted threats.

This month’s study shows that although G. biloba hasn’t changed much in appearance, it’s been evolving at a great rate at the genetic level. What the scientists learned, and the methods they used, will help us sort out other large genomes.

How we’ll use that knowledge — is up to us. I’ve decided to see it as another opportunity for “greater admiration.”

More posts looking at life’s long story:

• “Right-Handedness and Evolving Jaws”
  (October 28, 2016)
• “Sweet Potatoes, Genes, and Long Life”
  (October 21, 2016)
• The Minden Monster, What Killed Lucy”
  (September 23, 2016)
• “Brogdar, Öetzi, and Piltdown Man”
  (August 26, 2016)
• “Early Agriculture, New Tech”
  (July 22, 2016)

¹ Olives, olive oil, and a plant disease:

• Wikipedia
  • Xylella fastidiosa
  • Olive oil
    • Production and consumption
    • Global consumption
  • Olive
• “First reports of Xylella fastidiosa in the EPPO region”
  Special Alert, European and Mediterranean Plant Protection Organization (EPPO)

² Gene-swapping and X. fastidiosa’s genes:

• Wikipedia
  • Bacteriophage
  • CRISPR
  • Genetic engineering
    • History
  • Genetically modified organism
  • Horizontal gene transfer
  • Mobile genetic elements
• “The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.”
  Simpson AJ, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LM, Araya JE, Baia GS, Baptista CS, Barros MH, Bonaccorsi ED, Bordin S, Bové JM, Briones MR, Bueno MR, Camargo AA, Camargo LE, Carraro DM, Carrer H, Colauto NB, Colombo C, Costa FF, Costa MC, Costa-Neto CM, Coutinho LL, Cristofani M, Dias-Neto E, Docena C, El-Dorry H, Facincani AP, Ferreira AJ, Ferreira VC, Ferro JA, Fraga JS, França SC, Franco MC, Frohme M, Furlan LR, Garnier M, Goldman GH, Goldman MH, Gomes SL, Gruber A, Ho PL, Hoheisel JD, Junqueira ML, Kemper EL, Kitajima JP, Krieger JE, Kuramae EE, Laigret F, Lambais MR, Leite LC, Lemos EG, Lemos MV, Lopes SA, Lopes CR, Machado JA, Machado MA, Madeira AM, Madeira HM, Marino CL, Marques MV, Martins EA, Martins EM, Matsukuma AY, Menck CF, Miracca EC, Miyaki CY, Monteriro-Vitorello CB, Moon DH, Nagai MA, Nascimento AL, Netto LE, Nhani A Jr, Nobrega FG, Nunes LR, Oliveira MA, de Oliveira MC, de Oliveira RC, Palmieri DA, Paris A, Peixoto BR, Pereira GA, Pereira HA Jr, Pesquero JB, Quaggio RB, Roberto PG, Rodrigues V, de M Rosa AJ, de Rosa VE Jr, de Sá RG, Santelli RV, Sawasaki HE, da Silva AC, da Silva AM, da Silva FR, da Silva WA Jr, da Silveira JF, Silvestri ML, Siqueira WJ, de Souza AA, de Souza AP, Terenzi MF, Truffi D, Tsai SM, Tsuhako MH, Vallada H, Van Sluys MA, Verjovski-Almeida S, Vettore AL, Zago MA, Zatz M, Meidanis J, Setubal JC.; Abstract, Nature; via PubMed, NIH (July 13, 2000)

³ Ginkgos, really old trees:

• Wikipedia
  • Ginkgo
  • Ginkgo biloba
    • Palaeontology
    • History
      • Hiroshima
    • 1000-year-old ginkgo at Tsurugaoka Hachimangū
  • Ginkgoales
  • Permian
  • Tsurugaoka Hachimangū
    • The giant ginkgo
• “Permian ginkgophyte fossils from the Dolomites resemble extant O-ha-tsuki aberrant leaf-like fructifications of Ginkgo biloba L.”
  Fischer TC, Meller B, Kustatscher E, Butzmann R; BMC Evolutionary Biology (November 3, 2010); via PubMed/NCBI/NIH
• “Ginkgoales: Fossil Record”
  University of California Museum of Paleontology