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Editorial

10 Reasons to be Tantalized by the B73 Maize Genome

  • Virginia Walbot mail

    walbot@stanford.edu

    Affiliation: Stanford University, Stanford, California, United States of America

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  • Published: November 20, 2009
  • DOI: 10.1371/journal.pgen.1000723
  • Featured in PLOS Collections

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Copy of the press release originally distributed on November 16, 2009

Posted by PLoS_Genetics on 24 Nov 2009 at 16:16 GMT

PLoS Genetics 2009 Maize Genome Collection

Maize is an important crop in many countries of the world. It is widely used for human consumption, animal feed, and industrial materials. It also is considered an exemplar plant species for studying domestication, molecular evolution, and genome architecture. The authors of the research presented in this special collection used the first description of the B73 maize genome to probe some of the most intriguing questions in genetics and plant biology. The ten papers consider maize centromeres, new insights into transposon types and distribution, the abundance of very short FLcDNAs encoding predicted peptides, and many other “genetic jewels”.

A series of related papers, also embargoed until 2PM US Eastern Time, Thursday, 19 November 2009, will appear in the journal Science. These papers are available to registered reporters at <http://www.eurekalert.org...>. For more information, please contact Natasha Pinol, npinol@aaas.org, or
+1-202-326-7088.

The Physical and Genetic Framework of the Maize B73 Genome Wei F, Zhang J, Zhou S, He F, Schaeffer M, et al.
Wei et al. present a detailed account of how the maize genome was sequenced and how the maize chromosome-based pseudomolecules were constructed. In an approach that can be adopted in other large-genome species, the researchers use a comprehensive physical and genetic framework map to develop a minimum tiling path of over 16,000 BAC clones across the maize B73 genome.

A Genome-Wide Characterization of MicroRNA Genes in Maize Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, et al.
MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth, development and stress response. Zhang et al. provide a comprehensive analysis of maize miRNA genes and describe results suggesting that mature miRNA genes were highly conserved during their evolution.

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome Wei F, Stein J, Liang C, Zhang J, Fulton RS, et al.
By extensively analysing ~1% of the maize genome, Wei et al. demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets.

A Single Molecule Scaffold for the Maize Genome Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, et al.
The construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules. "The maize optical map is by far the most complex example of genome analysis via single molecules," says Dr. David Schwartz of the University of Wisconsin-Madison. "It was created using completely de novo techniques which greatly surpass conventional sequencing
and all available next-generation sequencing methods and platforms in terms of completeness, speed, accuracy and cost. This work points the way for
new platforms dealing with personal genomics."

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, et al.
There is a growing appreciation for the role of genome structural variation in creating phenotypic variation within a species. Springer et al. used comparative genomic hybridization to compare the genome structures of two maize inbred lines, B73 and Mo17, and observed that whole genes are missing in one inbred relative to the other. The data reinforce the view that maize is highly polymorphic (assuming different forms) but also show that there are often large genomic regions that have little or no variation.

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, et al.
To complement the completion of sequencing the maize B73 genome, Soderlund et al. sequenced 27,455 full-length cDNAs from two maize B73 libraries, representing the gene transcripts from most tissues and common abiotic stress conditions. They discovered about 1,600 unique maize genes, not found in other plant databases, that they anticipate will allow a better understanding of the biology and production of maize and cereal crops.

Loss of RNA-dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, et al.
Jia et al. focus on a mechanism by which the activity of genes and transposons alike are reined in or left to run free. The mechanism, involving small RNA molecules and their interactions with chromatin, is known to regulate transposons. Based on these findings, it now appears to influence gene activity as well.

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-localize with Epigenetic Marks for Open Chromatin across the Maize Genome Liu S, Yeh C-T, Ji T, Ying K, Wu H, et al.
Eighty-five percent of the newly sequenced maize genome consists of transposable elements, restless chunks of DNA that restructure the genome, generate genetic diversity, and influence gene expression patterns. Liu et al. debut a new PCR-based strategy for identifying Mu transposon insertion sites using highly conserved signature sequences from these elements. The finding that both Mu insertions and meiotic recombination sites concentrate in genomic regions decorated with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome Baucom RS, Estill JC, Chapparro C, Upshaw N, Jogi A, et al.
Baucom et al. report results showing that the maize genome provides a great number of different niches for the survival and generation of a wide variety of retroelements that have evolved differentially to occupy and exploit this genomic diversity. “This research breaks a lot of new ground in the understanding of what drives the evolution of most of the DNA in a chromosome. Although the work focuses on maize, the results are pertinent across all organisms, including humans.”

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, et al.
Because centromeres - the point or region on a chromosome to which the spindle attaches during mitosis and meiosis - consist of highly repetitive DNA sequences, these regions are exceedingly difficult to map and thus usually the last genomic regions to be assembled in genome projects. Using a comprehensive and general approach for mapping centromeres, Wolfgruber and colleagues precisely mapped all ten maize centromeres, constructed detailed maps of two centromeres, and determined the latter's present-day, as well as historic, boundaries. These findings that centromeres are dynamic loci that can shift over time have provided valuable insights into corn centromere evolution that may prove helpful in the design of artificial chromosomes of corn and other plants.

No competing interests declared.

RE: Copy of the press release originally distributed on November 16, 2009

PLoS_Genetics replied to PLoS_Genetics on 24 Nov 2009 at 16:31 GMT

The following links provide access to some of the news/blog coverage since publication. The journal is not responsible for the content of external sites; some external sites may require registration to view the full article; readers are welcome to judge the merits of each piece, considered in conjunction with the open-access article (http://www.plosgenetics.o...) for themselves.

Financial Times: <http://www.ft.com/cms/s/0...>

Nature News: <http://www.nature.com/new...>

Science News: <http://www.sciencenews.or...>

Scientific American: <http://www.scientificamer...>

Washington Post: <http://www.washingtonpost...>

No competing interests declared.

RE: Copy of the press release originally distributed on November 16, 2009

DovHenis replied to PLoS_Genetics on 26 Nov 2009 at 15:57 GMT

Corn Genome And More


A. From "Corn genome a maze of unusual diversity"
http://www.sciencenews.or...
Multiple teams announce complete draft of the maize genome, with a full plate of surprises that include hints about hybrid vigor.

- Although corn was domesticated only 8,000 to 10,000 years ago from the grass teosinte, the genetic diversity between any two strains of corn exceeds that found between humans and chimpanzees, species separated by millions of years of evolution. Much of the maize strains diversity is most probably due to the action of transposable elements, better known as jumping genes. Transposons and other repeated pieces of DNA make up 85 percent of the maize genome in the B73 strain, that has about 32,000 genes.

- Hybrid vigor: Often, when two inbred varieties of corn are crossed, the hybrid (shown center) is more robust and yields more than either parent (shown left and right). Corn's newly decoded genome may help scientists decipher the source of this hybrid vigor. In thousands of genes of B73/Mo17 maize strains hybrids, only the copy inherited from the male parent was active. This genetic phenomenon of only one parent’s gene being active is called imprinting. The researchers don’t know how or if imprinting contributes to hybrid vigor.

- The researchers also uncovered evidence that maize strains are CREATING NEW GENES and losing others. In fact, thousands of pieces of DNA found in one strain are completely missing from the other.

- “In other species, it’s a rare individual that has active transposons,” Walbot says, because active transposons have the potential to disrupt crucial genes. But the strategy has worked for corn, allowing its genome to nimbly adapt to changing environmental conditions, often from generation to generation. But, the species could also, eventually, split into multiple species.
Corn is living in peril, you might say. It has these features that allow flexibility in its genome, but there’s a cost to running this game.”


B. The subject obviously warrants the extensive multiple team effort and the data gleaned so far warrants a continuation of this grand project.

But a few remarks about the subject sciencenews report:

- An evolutionary contrast, for any purpose, of genomes of strains of corn domesticated only 8,000-10,000 yr ago with genomes of human-chimpanzee species separated by millions of years, is strange. The twain are not comparable. All genes-genomes, except human's, evolve by physiological adaptation to changing circumstance, whereas human genes-genomes, ONLY human genes-genomes, evolve in conjunction with change-control of circumstances. This is the ONLY evolved difference between humans and other organisms, THE difference that led also to virtual reality, i.e. to "spirituality".

( For religious persons, this may be the idea of Genesis 1:26. "Then God said Let Us make man in Our image, according to Our likeness; and let them rule over the fish of the sea and over the birds of the sky and over the cattle and over all the earth, and over every creeping thing that creeps on the earth". OK, let's not deal with How Man Rules...)

- Researchers don’t know how or if imprinting contributes to hybrid vigor? Genetics don't initiate a course of expression modifications (unless by accident). It is the corn's culture, its vigor, that leads to the genetic modifications, to modified expressions, by feedback to the genome. The feedback is "Replicate with change, here is a case of proven augmented energy constrainment". This mode of Life's normal evolution is the mode of energy-mass evolution universally. Survival ( from reverting to energy ) is the moto of each and every form of mass in the universe, not only of life.

- Evidence that maize strains are CREATING NEW GENES?

- “In other species, it’s a rare individual that has active transposons”. Maybe the genetic uniqueness of corn is a result of its extensive and varied cultivation, and maybe its apparent genetic male imprinting is in fact a result of best survival expression at given circumstances...


Dov Henis
(Comments From The 22nd Century)
Updated Life's Manifest May 2009
http://www.the-scientist....
Implications Of E=Total[m(1 + D)]
http://www.the-scientist....

No competing interests declared.