How Much of Our Genome Is Sequenced?

I'm getting ready for a class on the size and composition of the human genome so I thought I'd check to see the latest estimate of its size. Recall that in an earlier posting I concluded that the size of the human genome was 3,200,000,000 bp (3,200,000 kb, 3,200 Mb, 3.2 Gb) [How Big Is the Human Genome?].

You might think that all you have to do is check out the human genome websites and look up the exact size. That doesn't work because not all of the human genome has been sequenced and organized into a contiguous assembly of 24 different strands (one for each chromosome). So that prompts the question, how much of the human genome has actually been sequenced?¹

The latest assembly is GRCh37 Patch Release 7 (GRCh37.p7), released on Feb. 3, 2012. If you look at the data for this assembly you will see an estimate of the "Total Sequenced Bases in the Assembly." The number is 3,173,036,847 bp or 3.17 Gb. This value is close to estimates of the genome size from the years before the first draft of the genome sequence was published.

I was suspicious of this number since we know that there are many gaps in the human genome sequence. The largest gaps cover highly repetitive parts of the genome—mostly around the centromeres and other heterochromatic regions. There were also gaps at the locations of several gene clusters (e.g. ribosomal RNA genes) where it's impossible to determine the exact number of copies. In the case of ribosomal RNA gene clusters, these gaps have now been closed.

Deanna Church posted a few comments on my earlier posting. She's with the Genome Reference Consortium (GRC). That's the group responsible for updating the human genome. Deanna explained that "Total Sequenced Bases in the Assembly" is not an accurate representation of the truth.² What it actually means is total sequenced bases plus estimated sizes of the gaps. In other words, it's a good estimate of the size of the genome.

So, how much of the genome is actually sequenced and organized into "scaffolds," or contiguous stretches of DNA? You can see the actual numbers by clicking on Ungapped Lengths on the NCBI website.

The total number of sequenced base pairs that have been organized into scaffolds and placed on a particular chromosome is 2,861,332,606 bp. An additional 6,110,758 bp have been sequenced but the blocks of sequence cannot be placed in the assembly. Most of this unassigned sequence is on chromosomes 1,4,9, and 17 but some of it can't even be associated with a particular chromosome.

If we assume that the true haploid genome size is 3.2 Gb, or 3,200 Mb, then the sequenced and assigned part of the genome represents 89.6% and the unassigned sequenced part is 0.2%.

We can say that only 90% of the human genome has been sequenced and the remaining 10% falls into 357 gaps scattered throughout the genome. (Every chromosome has unsequenced gaps but some have more than others and it doesn't depend on the size of the chromosome.)

The The Wellcome Trust Sanger Institute is part of the Genome Reference Consortium but it maintains its own website on the human genome [Whole Genome]. The data on the e!Ensembl page refers to build CRCh37.p5 from Feb. 2009 but it also says the data was updated in Dec. 2011.

According to the Sanger Institute, the size of the sequenced genome is 3,283,984,159 bp and the "golden path length" is 3,101,804,739 bp. I've tried to find out what these numbers mean but if the information is present on the Ensembl website then it's very well hidden.

Are you interested in the number of genes? Here's the data from Ensembl. It indicates that the human genome contains 33,399 genes! [What Is a Gene?] [What is a gene, post-ENCODE?] This inflated value is calculated by including 12,523 genes that make an RNA product that's not translated. This is almost certainly a highly inflated number.

The data indicates that there are 181,744 gene transcripts or between 5 and 9 transcripts per gene depending on how you count the genes. I don't believe there are this many biologically functional transcripts per gene. I think the actual number is much closer to one (1) [Genes and Straw Men].

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1. It certainly doesn't "beg the question." That means something else entirely [Begging the Question].

2. That's a euphemism for "It's a lie!"

Monday's Molecule #158

 

This molecule is responsible for one of the distinguishing features of an entire group of species. Sadly, most undergraduates have never heard of this molecule and they never study the fundamental process that it represents. In my experience, about 90% of all introductory biochemistry courses skip the relevant chapter(s) in the textbooks. There's no reasonable excuse for that omission. It's just bad teaching.

Identify the molecule—the common name will do. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is phycocyanobilin the light absorbing pigment in cyanobacteria (and some other species). This blue pigment is found in large structures called phycobilosomes and it is the reason why cyanobacteria were called blue-green algae. The winners are Thomas Ferraro and Charles Motraghi (undergraduate).

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan

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An Ode to λ

 

I grew up in the phage group and spent many summers at the phage meetings in Cold Spring Harbor. Back then (late 1960s, early 1970s), the best scientists worked on bacteriophage λ (lambda) and the rest of us just tried to keep up.

A number of key insights in molecular biology came from studying this small virus that infects Escherichia coli and if you didn't know about that research you were really out of the loop.

But by 1990 it was already apparent that a new generation of students was growing up in ignorance of the fundamental concepts learned from studying bacteriophage and bacteria. I remember asking a class what they knew about the genetic switch in bacteriophage λ and getting nothing but blank looks! Everyone worked on eukaryotes by then and the knowledge acquired by the phage group was not relevant.

I tried to teach that knowledge in my classes. In my textbook I devoted 27 pages to describing the regulation of phage genes (in a chapter on "Gene Expression and Development"). Other instructors didn't care.

Here's a short list of things we learned from studying λ. How many have you learned?

Carnival of Evolution #44

This month's Carnival of Evolution (44th version) is hosted by The Atavism, a blog written by David Winter, a PhD student in evolutionary genetics [Proceedings of the 44th Carnival of Evolution].

Welcome to the 44th monthly meeting of the Society for the Blogging of Evolution. As you can see below, we had a large number of submissions this month and, in order to have only a single track of talks and get people to the banquet with sufficient energy to enjoy themselves, some submissions have been included in a poster session following the last of the talks. Submissions were grouped purely on their subject material, and a submission included in the poster-session shouldn't be viewed as inferior to any featured as a talk.

I hope you enjoy a day's worth of reading, and remind you that a host is still required for next month's meeting. Sign up with Bjørn (bjorn[at]bjornostman.com) if you are interesting in helping out.

The next Carnival of Evolution (March) needs a host. Contact Bjørn Østman at Carnival of Evolution if you want to volunteer. Meanwhile, you can submit your articles for next month's carnival at Carnival of Evolution.

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The Arsenic Affair: No Arsenic in DNA!

The "arsenic affair" began with a NASA press conference on Dec. 2, 2010 announcing that a new species of bacteria had been discovered. The species was named GFAJ-1 (Get Felisa a Job), by the lead author Felisa Wolfe-Simon. GFAJ-1 was grown in a medium that lacked phosphate and contained high concentrations of arsenic. The paper, published that day on the Science website, claimed that arsenic was replacing phosphorus in many of the cell's molecules, including nucleic acids.

Here's a (bad) video of the press conference. The high quality version from NASA is no longer available and some other YouTube videos don't allow embedding.

A Mormon Tale: The Romney Connection

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale

• Glasgow to Ontario
• Ontario to Nauvoo
• Nauvoo to Utah
• The Romney Connection

The Romney Connection

Hannah Hood Hill arrived in Salt Lake City when she was eight years old. She lived there with her father Archibald Newell Hill and his four wives. (Hannah’s mother, Isabella Hood, died at Winters Quarters in 1847.)

On May 10, 1862 Hannah Hood Hill married Miles Park Romney. Miles was born on August 18, 1843 in Nauvoo. His parents had been converted to the Church of the Latter Day Saints while living in England

Miles Romney (1806-1877) and his wife Elizabeth Gaskell (1809-1884) lived in the Liverpool area. Following their baptism, they sailed for New Orleans and made their way up the Mississippi by steamboat arriving at Nauvoo in 1841. This was a year before the Hill family arrived with Hannah Hood Hill.

The Hill family moved directly to Utah when Nauvoo was evacuated but the Romney family went to Missouri where they moved around from town to town until finally settling in St. Louis. In 1850, they were able to afford the move to Salt Lake City, Utah where they became reacquainted with the Hill family. Miles Park Romney was seven years old and Hannah Hood Hill was eight or nine.

Miles and Hannah had eleven children including Gaskell Romney (1871-1955). Miles Park Romney was sent on a mission to England Before their first child (Isabell 1863-1919) was born. While in England he preached for several years in the area around Liverpool (former home of his parents). He came back to Salt Lake City with a boatload of new English converts.

A Mormon Tale: Navoo to Utah

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale

• Glasgow to Ontario
• Ontario to Nauvoo
• Nauvoo to Utah
• The Romney Connection

Nauvoo to Utah

It was 1846 and the Mormons were preparing to leave Nauvoo for Utah. Many of them had crossed the Mississippi the previous year to prepare for the trip west. The Mormon town of Montrose, Iowa, had been settled some years earlier but now its population swelled to several thousand. Many blacksmiths, carpenters, and wainwrights set up shops to build wagons and carts.

The main exodus from Nauvoo began on February 4, 1846 with an advance party under Brigham Young. Archibald Newell Hood and his brother, Alexander Hill, were part of this advance party. The plan was to make it to Utah and establish a colony to receive the main body that would arrive later in the year. Here’s the description of what happened from the Wikipedia article on The Mormon Trail.

Monday's Molecule #157

 

You need to pay close attention in order to identify this molecule correctly.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is L-sedoheptulose 1,7-bisphosphate or L-altro-hept-2-ulose 1,7-bisphosphate. The D isomer is part of the pentose phosphate cycle and the Calvin cycle. The winner is Peter Monaghan.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller

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A Mormon Tale: Ontario to Nauvoo

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale

• Glasgow to Ontario
• Ontario to Nauvoo
• Nauvoo to Utah
• The Romney Connection

Ontario to Nauvoo

When we ended the first installment there were two families from Scotland living in Tosorontio township and Nottawasaga Township in southern Ontario. The Hood family and the Hill family came over from Scotland and settled originally in Dalhousie, in eastern Ontario. They moved south in the 1830s.

On April 6, 1832, Alexander Hill (born in 1811 in Scotland) married Agnes Hood (born in 1811 in Scotland). On Feb. 21, 1840, Isabella Hood (born in 1821 in Ontario) married Archibald Newell Hill (born in Scotland). They were married in Tosorontio where the Hill family farms were lcoated. Two brothers married Hood sisters. We are interested in the children of Isabella and Archibald. Recall that Isabella is the sister of William Hood and my wife and children descend from William.

UPDATE: The person in the photo is NOT the Isabella Hood Hill who is the mother of Hannah and the ancestor of Mitt Romney. Instead, it's the daughter of Isabella's sister who married Alexander Hill (see comments).

Archibald Newell Hill and Isobel Hood had two children while living in Canada. Samuel Hood Hill was born in Tosorontio on Dec. 23, 1840. Hannah Hood Hill was born in Tosorontio on July 9, 1842. She died in Colonia Juarez, Mexico in 1929 but a lot of interesting things happened in her life between those dates.

Religion is not on her radar ... and neither is something else

 

Heather Mallick published a column in today's Toronto Star where she declares that she is an atheist [Atheists should make more noise]. Good for her. We need more people to come out of the closet.

Why is she an atheist? It's not because she's opposed to religion it's because religion just isn't "on her radar." She just doesn't care about religion. In this sense she's not much different than most atheists: it's not that they actively study and reject any particular religion, they just don't believe in any gods.

I find it a bit strange that she and her husband ignore religion entirely. That seems like a recipe for disaster since religion is behind a lot of strife in today's world. But that's not what caught my eye when she described the topics that she and her husband do cover. There's seems to be a huge gap ... can you spot it? What else is sitting on the kitchen table?

If you like to stay current, you can’t simultaneously juggle all the elements that make up the news of the world. I follow politics, the arts, memoir and European history, with a minor in Spanish novelists, British comedy and American popular culture. My husband does economics, the history of the English language, meat-based cuisine, the novels of Graham Greene and soccer. The children have assigned themselves music, American fiction, social media and legal issues.

Religion sits on the kitchen table, orphaned.

I still love reading her columns in spite of her obvious deficiency!

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A Mormon Tale: Glasgow to Ontario

My wife and our children are cousins of Mitt Romney. This is the story of their common ancestor James Hood and his Mormon descendants.A Mormon Tale

• Glasgow to Ontario
• Ontario to Nauvoo
• Nauvoo to Utah
• The Romney Connection

Glasgow to OntarioJames Hood was born on April 6, 1776 in Kelso, a small town south of Edinburgh near the border with England. His parent were William Robert Hood (1744-1799)¹ and Hannah Clarke (1752-1832). James had six sisters (Agnes, Isabella, Margaret, Elizabeth, Hannah, and Mary) and one brother Dr. William Hood.

About five years after James was born, the family moved to Bridgeton in Barony Parish . At the time, Bridgeton was a small village, just north of the city of Glasgow. William Hood was employed there as a weaver and it’s quite likely that James also became a weaver at one of the factories in Barony.⁵

James Hood married Elizabeth Jones (1776-1803) in Barony on May 28, 1798. James and Elizabeth were both 22 years old. They had five children: William (1799-1894) (the direct ancestor of my wife and children), Jane (1800-1862), Elizabeth (1801-1875), Hannah (1802-1830), and Jean (1803-1803). Baby Jean dies shortly after birth and her mother, Elizabeth Jones, did not survive birth complications.

Evolution of Horseshoe Crabs

The IDiots are at it again but this time they are aided and abetted by scientists who should know better. The subject is horseshoe crabs, famous as "living fossils" because species that look similar to the four living species were around millions of years ago.

The BBC (United Kingdom) is broadcasting a new television series called "Survivors"¹ staring this month. The first episode is Horseshoe crabs are one of nature’s great survivors. The show is based on a book by Richard Fortey of the Natural History Museum in London, England.

Here's a quotation from the BBC press release where Fortey attempts to explain why horseshoe crabs haven't evolved.

A strange evolution?

Evolution not only brings about ‘improvements’ in body shapes and design that help a species adapt better to its surroundings. It also allows some species to remain basically the same.

‘These creatures tell us that evolution does not move inevitably forwards towards new morphology and new designs,' comments Fortey.

'Evidence for evolution is also found in past designs that endure to the present day. As long as the right habitat endures, then so will some of the creatures that inhabited the distant past.

The Problem With Press Releases

 
Press releases are a problem. Ryan Gregory has found a doozy: Radical Theory Explains the Origin, Evolution, and Nature of Life, Challenges Conventional Wisdom.

You may be tempted to actually read the paper. Don't. First, read what PZ Myers has to say: The comparison to jabberwocky is inevitable.

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Paul Doty (1920 - 2011) and DNA Renaturation

Paul Doty was born in 1920. He died last month (Dec. 5, 2011) at his home in Cambridge, Massachusetts, USA [Paul Mead Doty (1920-2011)]. He was a Professor at Harvard for most of his career.

For many of us, Doty's major contribution to molecular biology was his study of DNA renaturation with his long-time post-doc and collaborator, Julius Marmur (1926 - 1996)¹, a graduate of McGill University in Montréal, Canada. The paper that most of us remember is Marmur and Doty 1962: "Thermal Renaturation of Deoxyribonucleic Acids." This was the first time that the renaturation of complex DNA had been studied in detail and the results have led to many of the common techniques in use today.

Where Is David Attenborough?

 
Jerry Coyne has a little quiz for you as you watch this music video about evolution [An Evolution Music Video]. You should visit his blog website and answer the questions. Sandwalk readers should be able to answer the most difficult question namely, "Figure out where Attenborough is walking at the beginning: it’s a very famous place."

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