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
 Plant Science Research: St. Paul, MN
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    CareersSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Midwest Area St. Paul, Minnesota Plant Science Research Research





- Samac, Deborah - Debby
- Grass, Forage, and Rangeland Agroecosystems (215)

Research Project: **Location:
                            Plant Science Research** Project Number: 5062-21500-001-017-S
                        
                        Project Type: Non-Assistance Cooperative Agreement Start Date: Aug 1, 2023
                        
                        End Date: Jul 30, 2025 **Objective:**
                        
                        1: Annotate the genome assembly of RegenSY27x.
2: Identify the core and accessory genome of alfalfa. **Approach:**
                        
                        Tissues from RegenSY27x were collected and used for transcript profiling with RNA- Seq and Iso-Seq. The RNA-Seq data will be aligned using HISAT2 and assembled into transcripts using StringTie2 by collaborators. These assembled transcripts and full-length Iso-Seq transcripts will be used in structural annotation of gene space. The resulting gene annotations will be used to train parameters for de novo gene prediction using a variety of established gene prediction tools. Functional annotation will be done using all of the available protein databases Transcript abundance and differentially expressed genes in each tissue will be quantified using the RNA-Seq data and Iso-Seq data will be used to identify alternatively spliced genes, long non-coding RNAs, precursors of microRNAs, and tissue-specific isoforms.


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