Archaeology / Cultural Heritage

[Archaeology] [twocolumns]

Anthropology / Human Evolution

[Anthropology] [twocolumns]

Palaeontology / Earth Sciences

[Palaeontology] [twocolumns]

Evolution / Genetics

[Evolution][twocolumns]

African clawed frog genome contains 2 full sets of chromosomes from 2 extinct ancestors


Millions of years ago, one species of frog diverged into two species. Millions of years later, the two frogs became one again, but with a few extra chromosomes due to whole genome duplication. Such is the curious case of the African clawed frog, Xenopus laevis, a frog whose genome contains nearly double the number of chromosomes as the related Western clawed frog, Xenopus tropicalis.

African clawed frog genome contains 2 full sets of chromosomes from 2 extinct ancestors
Though similar in appearance, the tetraploid Xenopus laevis adult female is noticeably larger than its counterpart 
in the related diploid species Xenopus tropicalis [Credit: 2016 Shuji Takahashi]
In the evolution of species, different events have occurred over millions of years that have increased the number of chromosomes in some organisms. Polyploidy describes an event that increases the number of copies of each chromosome. Vertebrates have undergone at least two different polyploidy events since their original divergence. While it is relatively rare nowadays to observe a mammal, reptile or bird with an abnormal number of chromosomes, polyploidy is common in fish, amphibians and plants.

Prof. Daniel Rokhsar, Professor of Genetics, Genomics and Development at the University of California, Berkeley and head of the Molecular Genetics Unit at the Okinawa Institute of Science and Technology Graduate University (OIST), Prof. Masanori Taira from the University of Tokyo and Prof. Richard M. Harland from the University of California at Berkeley led groups of researchers in examining the genome evolution of the African clawed frog. This large, collaborative project included scientists from a variety of universities and institutions across the globe. The study, published in Nature and featured on the cover, revealed that the X. laevis genome is composed of two different sets of chromosomes from two extinct ancestors.

African clawed frog genome contains 2 full sets of chromosomes from 2 extinct ancestors
'Fossil' DNA sequences found only in the S subgenome (chromosomes) ofXenopus laevis emit a red glow employing the 
FISH method. The nine Schromosomes here clearly possess a larger number of red regions, believed tohave derived 
from ancestral species S. (Chromosome 9, at bottom right, isrepresented as '9_10,' as it corresponds to the fusion
 of ancestralchromosomes corresponding to chromosomes 9 and 10 in Xenopus tropicalis) 
[Credit: 2016 Yoshinobu Uno]
Dr. Oleg Simakov, a postdoctoral scholar in the Molecular Genetics Unit at OIST, developed an algorithm to determine the length of time, in millions of years, between the divergence and subsequent fusion of the X. laevis ancestral species. In order to be able to calculate these times, the X. laevis genome had to be correctly annotated. Annotation involves identifying which regions of DNA contain coding genes or non-coding regions. While automation can simplify this process, many mistakes are made.

Dr. Yuuri Yasuoka of the Marine Genomics Unit at OIST helped to manually correct the gene annotation. His graduate studies at the University of Tokyo under the guidance of Prof. Masanori Taira allowed him to develop the skills necessary for his role in this project. "Taking advantage of my experiences on the field of developmental biology, I examined genes involved in developmental processes," he clarified.

African clawed frog genome contains 2 full sets of chromosomes from 2 extinct ancestors
Two ancestral species with nine pairs of chromosomes, S and L, mate to produce a hybrid S/L offspring with 18 
chromosomes that do not pair. This sterile offspring undergoes whole genome duplication to produce a new 
fertile species with 18 pairs of chromosomes that is ancestral to all Xenopus species. For clarity, the
 process is rendered here with only one type of chromosome 
[Credit: 2016 Masanori Taira]
Dr. Adam Session, a former graduate student in Prof. Rokhsar's lab at the University of California at Berkeley and co-lead author of the Nature publication, elaborated "The most exciting finding from our study is that we can partition the current X. laevis genome into two distinct sets of chromosomes, each descended from a unique ancestral species. While plant studies have been able to show similar results using related species still in existence, this study is the first time this has been done with two extinct progenitor species."

This large collaborative project resulted in new knowledge of genome duplication that can be applied to evolutionary studies of other organisms. "Because X. laevis is a well-studied model system for cell and developmental biology, it is ideal for to studying the effect of polyploidy on evolution," Dr. Simakov explains.

Source: Okinawa Institute of Science and Technology (OIST) Graduate University [October 19, 2016]
TANN

Post A Comment
  • Blogger Comment using Blogger
  • Facebook Comment using Facebook
  • Disqus Comment using Disqus

No comments :


Exhibitions / Travel

[Exhibitions] [bsummary]

Natural Heritage / Environment / Wildlife

[Natural Heritage] [list]

Astronomy / Astrobiology / Space Exploration

[Universe] [list]