Title: Annotation data from: Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata (Asteraceae), a keystone species of western North America
	DOI: 10.7923/hysd-x388
	RCDS ID: 37bdbf18-c36d-4a61-8cd5-c82bc7443622

Data, code and/or products within this dataset support the following manuscript:
	Manuscript Title: Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata (Asteraceae), a keystone species of western North America  
	Journal: American Journal of Botany
	DOI: ###Pending Review

Description/Abstract:
	Supporting dataset for genome assembly data found within NCBI BioProjects PRJNA1032953 (UTT2), PRJNA722258 (IDT2) and PRJNA795150 (IDT3-Reference Genome). Fasta assembly data used in the EDTA analysis to generate subsequent output files are available from the NCBI Genome database and raw sequence data are available from the NCBI SRA database. Each input fasta contains the nine pseudo-chromosomes described in [Melton et al. 2022](https://doi.org/10.1093/g3journal/jkac122). Reads from each sample were mapped to the nine pseudo-chromosomes and used to call a consensus sequence. The EDTA analysis provides several outputs, listed below. The primary file of interest is the "SAMPLE_consensus.fasta.mod.EDTA.TEanno.gff3" file. This file was used as inputs for comparisons of TE content across the three genomes.

	Please visit https://github.com/oushujun/EDTA for more information about the EDTA pipeline.

	FILES:
	SAMPLE_consensus.fasta.mod.EDTA.TEanno.gff3 == Whole-genome TE annotation
	SAMPLE_consensus.fasta.mod.EDTA.TEanno.sum == Summary of whole-genome TE annotation
	SAMPLE_consensus.fasta.mod.EDTA.TElib.fa == A non-redundant TE library
	SAMPLE_consensus.fasta.mod.MAKER.masked == Low-threshold TE masking

	**Data Use**
	*License*:  
	Creative Commons Attribution International 4.0 ([CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/legalcode))
    *Recommended Citation*:
    Melton AE, Novak SJ, Buerki B. 2023. Annotation data from: Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata (Asteraceae), a keystone species of western North America [Data set]. University of Idaho. https://doi.org/10.7923/hysd-x388

    **Funding**
    US National Science Foundation and Idaho EPSCoR: OIA-1757324

Resource URL: https://data.nkn.uidaho.edu/dataset/annotation-data-utilizing-comparative-approach-assess-genome-evolution-during-diploidization

Creator(s):	
	1. Anthony E Melton
		Unique identifier: https://orcid.org/0000-0003-4882-6664
		Affiliation(s): Boise State University
	2. Stephen J Novak 
		Unique identifier: https://orcid.org/0000-0002-0537-7953
		Affiliation(s): Boise State University
	3. Sven Buerki
		Unique identifier: https://orcid.org/0000-0002-8299-6539
		Affiliation(s): Boise State University

Other Contributor(s): 
	1. Andrew Wright Child
	 	Unique identifier: https://orcid.org/0000-0001-6666-0739
		Affiliation(s): University of Idaho
		Role: Data manager

Publisher: University of Idaho

Publication Year: 2023
	
Language(s): American English

Subject(s):
	1 Natural Sciences
		1.6 Biological sciences

Keywords/Tags: 

Resource Type General: Dataset
		
Dates: NULL	

Date available for the public: 2023-11-29 

Sizes: 15GB
 
Format(s): gff, fa, sum, masked, txt, xml
 
Version: NULL

Funding References: 
	Funder Name: US National Science Foundation and Idaho EPSCoR
		Award Number: OIA-1757324
		Award Title: RII Track-1: Linking Genome to Phenome to Predict Adaptive Responses of Organisms to Changing Landscapes
		Award URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1757324
 
Spatial/Geographical Coverage Location: 
	Study Area Description: Utah and Idaho USA
		Easting: -109.3876
		Westing: -116.9641
		Northing: 43.3371
		Southing: 38.306
	Point Location(s): 
		UTT2: -109.3876, 38.306
		IDT3: -116.9641, 43.3366
		IDT2: -116.0081, 43.3371
 
Temporal Coverage: NULL
 
Granularity of the Data: NULL
 
Contact Info: 
	Contact Name: Sven Buerki
	Contact Email: svenbuerki@boisestate.edu 
 
Related Content:   
	Peer Reviewed Manuscript-American Journal of Botany | ###Pending Review

Data/Code Files:
	readme.txt: project metadata in readme.txt format
	hysd-x388.xml: project metadata in DataCite XML format
	UTT2: directory containing UTT2 data
		UTT2_consensus.fasta.mod.EDTA.TEanno.gff3
		UTT2_consensus.fasta.mod.EDTA.TEanno.sum
		UTT2_consensus.fasta.mod.EDTA.TElib.fa
		UTT2_consensus.fasta.mod.MAKER.masked
	IDT3: directory containing IDT3 data
		IDT3_consensus.fasta.mod.EDTA.TElib.fa
		IDT3_consensus.fasta.mod.EDTA.TEanno.gff3
		IDT3_consensus.fasta.mod.MAKER.masked
		IDT3_consensus.fasta.mod.EDTA.TEanno.sum
	IDT2: directory containing IDT2 data
		IDT2_consensus.fasta.mod.EDTA.TEanno.gff3
		IDT2_consensus.fasta.mod.EDTA.TEanno.sum
		IDT2_consensus.fasta.mod.EDTA.TElib.fa
		IDT2_consensus.fasta.mod.MAKER.masked