This Steier_README.txt file was generated on 2021-12-30 by Andrew Hopkins


GENERAL INFORMATION

1. Title of Dataset: STEIER_ET_AL_MEDICAGO_SECTION_BUCERAS_(LEGUMINOSAE)

2. Author Information
	A. Corresponding Author
		Name: Kelly Steele
		Institution: Science and Mathematics Faculty, Arizona State University Polytechnic
		Email: kpsteele@asu.edu

	B. First Author
		Name: Julia E Steier
		Institution: School of Life Sciences, Arizona State University 
		Address: Smithsonian Institution, Washington, D. C. 20002 USA
		Email: juliasteier93@gmail.com

	C. Author
		Name: Terezie Mandáková
		Institution: Central European Institute of Technology and Faculty of Science, Masaryk University 
		Email: Terezie.Mandakova@ceitec.muni.cz

	C. Author
		Name: Martin F Wojciechowski
		Institution: School of Life Sciences, Arizona State University 
		Email: Martin.Wojciechowski@asu.edu 

3. Funding Information

Support for this research was provided by intramural funding to KPS from
the College of Integrative Sciences and Arts and the Barrett Honors
College at Arizona State University, the School of Life Sciences at
Arizona State University to MFW, and by the CEITEC 2020 project (grant
no. LQ1601) to TM.

DATA & FILE OVERVIEW

1. File List: 
Steier_genome_size_data
	Steier_genome_size_calculations.csv
	Steier_genome_size_raw_data.tar.gz

Steier_supplemental
	Steier_Figure_S1.tiff
	Steier_Figure_S2.tiff
	Steier_Figure_S3.tiff
	Steier_Figure_S4.tiff
	Supplemental Table S1.xls
	

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 

Taxon Sampling - 
Of the 42 accessions of Medicago, 39 were 158 sampled for genome size
and 14 were sampled for  chromosome number. Most of the species within
sect. Buceras, particularly M. monantha, were  represented by multiple
accessions from various locations to sample across their geographic 
range.

Genome Size Estimation using Flow Cytometry —
Twelve of the 14 Medicago species studied were sampled for genome size,
six of which were sampled from multiple accessions. Seeds of the species
Glycine max (L.) Merr. cv. ‘Polanka’ and Raphanus sativus L. cv. ‘Saxa’,
used as known genome size standards, were obtained from J. Doležel
(Institute for Experimental Botany, Olomouc, Czech Republic; Doležel and
Bartos 2005) and seeds of a third species used as a standard, M.
truncatula cv. ‘Jemalong’, were obtained from the Medicago Hapmap
Project (http://www.medicagohapmap.org). Seedlings of all accessions
were grown in a growth chamber at 25°C under identical light and
humidity conditions. Nuclei from samples of fresh leaf tissue were
prepared following the procedure of Doležel and Bartos (2005) using
Galbraith’s buffer (Galbraith et al. 1983). Samples were analyzed on a
BD FACSCalibur flow cytometer at the Biodesign Institute, Arizona State
University (Tempe, Arizona). Mean DNA content was estimated on ca.
15,000 nuclei, with peak means identified using CellQuest software
(Becton Dickinson). Calculation of genome size in picograms (pg) used
the sample peak mean divided by the standard peak mean, multiplied by
the known genome size of the standard. Each plant accession was sampled
three or more times on different days to minimize the effect of
instrument drift and other variables. For most accessions three or more
different plants were sampled, but occasionally only one or two plants
were sampled (see Appendix 2). Values reported are averages of the
values obtained from each individual accession. The known standard
genome size values used were 1.15 pg for M. truncatula cv. Jemalong
(Blondon et al. 1994), 1.11 pg for Raphanus sativus cv. Saxa, and 2.3 pg
for the genome size of Glycine max cv. Polanka rather than the 2.5 pg
indicated in Doležel and Bartos (2005) based on results obtained with
other standards (Steele et al. in preparation). 


DATA-SPECIFIC INFORMATION FOR: 	Steier_genome_size_calculations.csv

1. Number of variables:		9

2. Number of cases/rows:	132

3. Variable List: 
sample		- sample name (numbered when more than one accession per species)
PI #		- accession identifier, Plant Introduction (PI) or Western Regional (W6)
G1 standard	- mean peak position on the fluorescence intensity axis (PP) of the standard 
G1 sample	- mean peak position on the fluorescence intensity axis (PP) of the sample 
2C standard	- known genome size of the standard used (pg/2C)
2C sample	- genome size of the sample (pg/2C), calculated by dividing
			  the sample peak mean (G1 sample) by the standard peak mean (G1
			  standard), multiplied by the known genome size of the standard (2C
			  standard)
std name	- name of the standard used (glycine, raphanus, or medicago)
sample #	- sample number within a batch of samples run on flow cytometer
date		- date that data was collected MM/DD/YYYY





DATA-SPECIFIC INFORMATION FOR: Steier_genome_size_raw_data.tar.gz

1. Number of files:		132

2. Description of files:
This file contains raw genome size data produced by flow cytometry for
each sample. An example of how to interpret these visualizations can be
found in "Steier_Figure_S1.tiff" (see below). 

Folders are named following the convention "sample_PI#". 

Files are named following the convention "MM_DD_YY.sample#.pdf"

Steier_flow_cytometry_raw_data_index.xlsx provides the sample, PI#,
date, and sample # for each sample and experiment





DATA-SPECIFIC INFORMATION FOR: 	Steier_Figure_S1.tiff

Representative example of raw genome size data produced by flow
cytometry. Location of peaks along the x-axis is used to calculate
genome size in picograms. Peak M1 represents the standard, Medicago
truncatula (cv. Jemalong), and peak M2 represents the experimental
sample. On the right is a M. monantha group 1 accession (35), showing a
smaller genome size and on the left is accession monantha 250, from M.
monantha group 2, which indicates a larger genome size.





DATA-SPECIFIC INFORMATION FOR: Steier_Figure_S2.tiff

Phylogram of tree number 1 of 1,000 equally most parsimonious trees (241
steps) produced in a heuristic search analysis of 49 nrDNA ITS and
plastid encoded 5’ trnK intron/matK gene sequences from the accessions
within “Dataset 2”. The scale bar indicates the number of substitutions,
and branch length is proportional to this value.





DATA-SPECIFIC INFORMATION FOR: Steier_Figure_S3.tiff

Chromosomes of (A) Medicago biflora (2n=16; accession #70), (B) M.
brachycarpa (2n=16; #72), (C) M. astroites (2n=16; #216), (D) M.
monspeliaca (2n=16; #247), (E-G) M. fischeriana (2n=14; #88, 266 and
267), (H-I) M. polyceratia (2n=28; #194 and 259), and (J-N) M. monantha
(2n=26, 30, 36, 44 and 44; #264, 35, 36, 249 and 250, respectively)
counterstained by DAPI (inverted in Adobe Photoshop). Arrowheads mark
the putative fusion chromosomes in M. fischeriana. Scale bars indicate
10 μm.





DATA-SPECIFIC INFORMATION FOR: Steier_Figure_S4.tiff

Map of locations of Medicago monantha accessions sampled in this study.
Collection locations are distinguished by the accession’s voucher
number, see Appendix 2. Unboxed numbers indicate geographic locations
where M. monantha group 1 accessions were collected. Boxed numbers
indicate geographic locations where M. monantha group 2 accessions were
collected. The dashed line represents the 45˚ longitudinal line that
Small and Fawzy (1992) concluded was a boundary between morphologically
distinct populations of M. monantha. Accession latitude and longitude
information was obtained from the USDA National Plant Germplasm System.
These data were plugged into the map-making application on
easymapmaker.com.





DATA-SPECIFIC INFORMATION FOR: 	Supplemental Table S1.xls

Accessions of Medicago species analyzed in this study. Species and
section names follow Small (2011); original identification in
parenthesis where applicable. USDA National Plant Germplasm System
accessions begin with PI or W6, any other accessions are from Ernest
Small’s collection, with seeds donated to K. P. Steele. Location
information obtained from the USDA National Plant Germplasm System, or
Ernest Small’s notes as summarized in Steele et al. (2010). Accessions
with “*” originated from a mixed USDA seed collection. Average genome
sizes listed in pg; +/- standard deviation with number of samples
analyzed for genome size estimation “N”. Chromosome numbers with “*”
were obtained from literature (Small 2011). For all columns, — indicates
data not available.
