Tall-Tree Genomes Sequenced

[lpetrich]

By now, so many species' genomes have been sequenced that another one is far from being news. But I couldn't resist this one.

California scientists unravel genetic mysteries of world’s tallest trees - SFChronicle.com
I've added to the article's list:

• Influenza virus: 13,500 base pairs
• Escherichia coli bacterium: 5 million bp's
• Brewer's yeast: 12 M bp's
• Fruit fly: 140 M bp's
• Walnut tree: 650 M bp's
• Human: 3 billion bp's
• Giant sequoia: 8 B bp's
• Coast redwood: 27 B bp's
• Axolotl salamander: 28.4 B bp's

“You think of plants generally — they don't have brains, so they can’t be that complicated, but a redwood has to stay in the same place for thousands of years and fight off everything that comes its way,” said Steven Salzberg, a professor of biomedical engineering at Johns Hopkins University in Baltimore, who skippered the sequencing work. “It has to have a pretty robust ability to fight off fungi, microbes, insects, beetles, and a vast array of temperatures and humidities.”

The plan now is to analyze the genes in multiple trees, identify their genetic traits and determine why some thrive and others don’t. Ultimately, the researchers hope to develop genetic variation models for the various groves of old growth.

“Now we can screen for genetic diversity and make restoration decisions,” said Emily Burns, the director of science for Save the Redwoods League. “We want to know which genes are influential for drought tolerance and fire resistance. It’s the road map for how we are going to conserve the species in the future.”

...
One tree in Redwood National and State Parks, near Crescent City (Del Norte County), is 2,520 years old. The largest of the Sierra sequoia giants, which generally live longer than their coastal cousins, is 3,240 years old, according to a Save the Redwoods League study.

 

[lpetrich]

Let's see why that recent sequencing is nothing unusual:
 Lists of sequenced genomes

•  List of sequenced eukaryotic genomes
  •  List of sequenced animal genomes
  •  List of sequenced fungi genomes
  •  List of sequenced plant genomes
  •  List of sequenced algae genomes
  •  List of sequenced plastomes
  •  List of sequenced protist genomes
• Prokaryotes:
  •  List of sequenced bacterial genomes
  •  List of sequenced archaeal genomes

 

[lpetrich]

The Bitter Truth: Scientists Sequence the Almond Genome - Scientific American

Cracking the nut’s “cyanide problem” could make it easier to cultivate sweeter varieties of this ancient snack

In many detective novels, the ominous aroma of bitter almonds foreshadows a swift demise. The kernels of wild almond varieties—and also the pits of peaches, cherries and other stone fruits—have chemical compounds that contain cyanide. Almond breeders have long endeavored to cultivate varieties that lack the potent poison, a process that can be expensive and time-consuming.

... Charting the nut’s genome allowed researchers to identify the protein that regulates the genes responsible for producing the toxin found in bitter wild almond varieties. The research may help farmers more efficiently breed out the toxin, which sometimes pops up in new domestic varieties of almonds and other crops.

Mutation of a bHLH transcription factor allowed almond domestication | Science -- that protein


Some more such genomic research:
Arabica Coffee Genome Sequenced | UC Davis
Genomic focus brings tea research to the boil - tea-shrub genome also sequenced

 

[lpetrich]

Ensembl species lists:

Species List (vertebrates)
Species List (invertebrates)
Species List (plants)
Species List (fungi)
Species List (protists)

JGI Genome Portal - Home - the Joint Genome Institute of the US Department of Energy
JGI GOLD | Home - the Genomes OnLine Database
JGI IMG Home - Integrated Microbial Genomes
Mycocosm - fungi
Phytozome v12.1: Home - plants

Home - Genome - NCBI at PubMed

It is hard to get a good overall view of what has been sequenced, though coverage of the tree of life has gradually been improving as more and more organisms get sequenced.

 

[lpetrich]

DNA Sequencing Costs: Data | NHGRI

The cost of sequencing a human-sized genome has dropped dramatically over the last 20 years, from when the Human Genome Project was a major achievement, to today, when it is routine. Our genomes have 3 billion base pairs of DNA in them, and printing them all in typical book print would require around a million pages. That's around 3000 typical books.

The cost of a single pass of sequencing a 3-billion-base-pair genome was about $100 million back in 2001, and it dropped to $10 million in 2017. It then dropped very fast to $10 thousand in 2010 and $1 thousand in 2011 before leveling off. It dropped rather fast in 2015 to $100 and it has been at that value ever since.


As genome sequencing has grown, genome sequencers have turned their attentions to environmental samples, including gut-contents samples. This is  metagenomics. One typically gets sequences of only some of the genes of the organisms in one's samples, but that is enough to identify many known organisms, and also many unknown ones. Hundreds of organisms are now only known from sequencing of environmental samples.