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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Research Project #444186

Research Project: Annotation and Analysis of the Alfalfa Genome

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

1: Annotate the genome assembly of RegenSY27x. 2: Identify the core and accessory genome of alfalfa.

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.