Category Archives: Transhuman News

RICHMOND - The Virginia Department of Forestry announced Monday that a team of scientists from across the nation has decoded the genome of a Virginia Loblolly pine tree.

With 22 billion base pairs, this is the largest genome ever sequenced. In comparison, the human genome has 3 billion base pairs.

Led by Dr. David Neale, professor of plant sciences at the University of California-Davis, the team used tissue from a single pine seedling obtained from the Virginia Department of Foresry and broke down the trees DNA into smaller, more manageable data pieces and analyzed them with a super-computer.

The team then re-assembled the pieces, figured out which genes were present, where they are on the genome, and what they do. This new approach, developed at the University of Maryland, enabled researchers to perform such a large and complex genome sequencing.

Its a huge genome, Neale said in a press release. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order. The contribution of a loblolly pine tree was critically important, not only for the genome sequencing but moreso for all those who follow and will now have completely open access to data and germplasm resources.

The Loblolly pine, grown in the orchard at the Forestry Department's New Kent Forestry Center, was selected for sequencing because of its broad distribution, economic value and long history of genetic research.

Original post:
Scientists use Loblolly pine seedling from New Kent to unlock largest genetic code ever sequenced

PUBLIC RELEASE DATE:

19-May-2014

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

Shenzhen, May 18, 2014---Chinese scientists from Chinese Academy of Agricultural Sciences and BGI successfully deciphered the genome sequence of another diploid cotton-- Gossypium arboreum (AA) after the completed sequencing of G. raimondii (DD) in 2012. G. arboreum, a cultivated cotton, is a putative contributor for the A subgenome of cotton. Its completed genome will play a vital contribution to the future molecular breeding and genetic improvement of cotton and its close relatives. The latest study today was published online in Nature Genetics.

As one of the most important economic crops in the world, cotton also serves as an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis. However, breeders and geneticists remain little knowledge on the genetic mechanisms underlying its complex allotetraploid nature of the cotton genome (AADD). It has been proposed that all diploid cotton species present may have evolved from a common ancestor, and all tetraploid cotton species came from interspecific hybridization between the cultivated species G. arboreum and the non-cultivated species G. raimondii.

After the completed sequencing of G. raimondii in 2012, researchers started the work on decoding the genome of G. arboreum. In this study, they sequenced and assembled the G. arboreum genome using whole-genome shotgun approach, yielding a draft cotton genome with the size of 1,694 Mb. About 90.4% of the G. arboretum assembled scaffolds were anchored and oriented on 13 pseudochromosomes.

Furthermore, researchers found the long terminal repeat (LTR) retrotransposons insertions and expansions of LTR families contributed significantly to forming the double-sized G. arboreum genome relative to that of G. raimondii. Further molecular phylogenetic analyses suggested that G. arboreum and G. raimondii diverged about 5 million years ago, and the protein-coding capacities of these two species remained largely unchanged.

To investigate the plant morphology mechanisms of cotton species, a series of comparative transcriptome studies were performed. Results suggested that NBS-encoding subfamilies played an essential role on the immune to Verticillium dahliae. The resistance of G. raimondii on Verticillium dahliae was caused by expansion and contraction in the numbers of NBS-encoding genes, accordingly the loss in the genome of G. arboreum was responsible to their susceptible.

Another interesting finding of this study is the cotton fiber cell growth, and they found the 1-aminocyclo-propane-1-carboxylic acid oxidase (ACO) gene was a key modulator. Researchers suggest the overproduction of ACO maybe the reason why G. raimondii have a poor production of spinnable fiber, while the inactivation of ACO in G. arboreum might benefit its fiber development.

The G. arboreum genome will be an essential reference for the assembly of tetraploid cotton genomes and for evolutionary studies of Gossypium species. It also provides an essential tool for the identification, isolation and manipulation of important cotton genes conferring agronomic traits for molecular breeding and genetic improvement.

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Chinese scientists crack the genome of another diploid cotton Gossypium arboreum