U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 close



Research
                Research Home
                            National Programs
                            Research Projects
                            Scientific Manuscripts
                            International Engagement
                            Scientific Software/Models
                            Databases and Datasets
                            Office of Scientific Quality Review
            Media
                News & Features
                            Multimedia
                            Briefing Room
                            Down on the Farm
                            Press Room
                            Science in Your Shopping Cart
                            Scientific Discoveries
                            Tellus
                            Under the Microscope
            About ARS
                About ARS Home
                            Staff Directory
                            Labs and Research Centers (Map)
                            Headquarter Offices
                            Organizational Chart
                            Employee Services (REE Employees Only)
                            Office of Outreach, Diversity, and Equal Opportunity
            Work With Us
                Work With Us Home
                            ARS Vacancies at USAJOBS
                            Careers at ARS Information
                            Scientific Collaborations
                            Extramural Agreements
                            1890 Faculty Research Sabbatical ProgramSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Research Publications at this Location





- ARS National Programs
- Search for a scientific manuscript
- Search for a research project
- ARS Software
- Programs and Projects
- Collaborations
- Subjects of Investigation
- Publications

Title:   Author  item
                                            Liu, Ge

                                                         - *George*item
                                            ALKAN, CAN - UNIVERSITY OF WASHINGTONitem
                                            JIANG, LU - University Of Marylanditem
                                            ZHAO, SHAYING - University Of Georgiaitem
                                            EICHLER, EVAN - HOWARD HUGHES MED INST.
  Submitted to: Genome Research
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 9/30/2008
                                    Publication  Date: 5/1/2009
                                    Citation: Liu, G., Alkan, C., Zhao, S., Eichler, E.E. 2009. Comparative Analysis of Alu Repeats in Primate Genomes. Genome Research. 19(5):876-885.Interpretive Summary: We previously did a large-scale comparative genome analysis on high-quality finished genomic sequence from cattle, dog, and human. We estimated the pattern, frequency, and nature of repetitive sequences and their contribution to the whole genome size. Differential turn-over patterns of lineage-specific or ancestral repetitive sequences were found to account for the overall size differences among cattle, dog and human genomes. In this study, we used one of the short intersperse repetitive elements -- Alu as an example to estimate their contributions to the primate genome architecture. With large-scale randomly sampled genome sequences now available, we performed an unbiased characterization of Alu repeats using these representative sequence data. We found that different distribution patterns exist in closely related primate species. We identified lineage specific Alu elements in nonhuman species which contain diagnostic mutations distinct from human counterparts. Our results supported that a burst of Alu activities occurred during the emergence of simians (35 million years ago) after the divergence of prosimians (55 million years ago), which confirmed the master genes hypothesis for Alu amplifications with individual lineage. These new lineage specific Alu subfamilies expand our understanding of Alu evolution and their contributions to primate genome architecture. This work provided us an established software platform to further analyze the transposable elements and their contribution in the emerging bovine genome assembly.
                                Technical Abstract: Background: Alu repeats are SINEs (Short intersperse repetitive elements) which enjoy a successful application in genome evolution, population biology, phylogenetics and forensics.  Human Alu consensus sequences were widely used as surrogates in nonhuman primate studies with an assumption that all primates share the same Alu elements.  With large-scale randomly sampled genome sequences becoming available, it is worthwhile to perform an unbiased characterization of Alu repeats in nonhuman primates using these representative sequence data.

Results: Using BAC (Bacteria Artificial Chromosome) end sequences and genomic sequences, we did a global assess of the divergence distributions, phylogenies and consensus sequences for both ancestral and lineage specific Alu elements in primates including lemur, marmoset, macaque, baboon, chimpanzee as compared to human.  We found that in prosimians like lemur, Alu elements had a more broad and symmetric distribution and displayed a slower decline in recent Alu activity.  While in simians, Alu elements had skewed distributions shifting to the ancient elements and accelerated declining rates in recent Alu activities.  Lineage specific Alu elements in lemur, marmoset, macaque and baboon contain diagnostic mutations distinct from human counterparts – Alu J, S and Y subfamilies, respectively.  These lineage specific Alu elements were estimated to emerge 15-27 mya (million years ago) and might be still active in their hosts.
 
Conclusions: Our results supported that a burst of Alu activities occurred during the emergence of simians (35 mya) after the divergence of prosimians (55 mya), which confirmed the master genes hypothesis for Alu amplifications with individual primate lineage.  These new lineage specific Alu subfamilies expand our understanding of Alu evolution and their contributions to primate and mammalian genome architecture.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov