Genomics of white and black fonio millets : passport data, snp and kmer files.

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Kaczmarek, Thomas; Cubry, Philippe; Champion, Louis; Causse, Sandrine; Couderc, Sandrine; Orjuela, Julie; Uyoh, Edak A.; Oselebe, Happiness O.; Dachi, Stephen N.; Adje, Charlotte; Sekloka, Emmanuel; Achigan-Dako, Enoch G.; Ibrahim Bio Yerima, Abdou R.; Saidou, Sani; Bakasso, Yacoubou; Diop, Baye M.; Gueye, Mame C.; Agyare, Richard Y.; Adjebeng-Danquah, Joseph; Gueye, Mathieu; Wieringa, Jan J.; Vigouroux, Yves; Billot, Claire; Barnaud, Adeline; Leclerc, Christian, 2024, "Genomics of white and black fonio millets : passport data, snp and kmer files.", https://doi.org/10.18167/DVN1/OYTQO6, CIRAD Dataverse, V1, UNF:6:Id37Yd1Os2wQVns323wx4g== [fileUNF]

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Description	Crop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. In Western Africa, two small indigenous grain cereals are found, black and white fonio (Digitaria exilis and Digitaria iburua respectively). The relationship between these two cultivated crops and wild Digitaria species is still unclear. We analysed whole genome sequences of 265 accessions comprising the two cultivated species and their closely wild relatives. We used different complementary methods and genomic approaches to unravel the domestication history of these fonio millets, which is key to support a process of valorisation of these native species while preserving the diversity necessary for future adaptations. We provide here the passport data, the vcf files, and the kmer files used to perform the analyses. Codes can be accessed in the CIRAD GitLab repository Two compressed VCF files are provided. They contain high quality biallelic SNPs. One is filtered for Minor Allele Frequency (MAF) at 5%. Both vcf.gz are associated to their corresponding index file .tbi Different extensions for the kmer analysis files are provided and correspond to the 1,000,000 k-mer presence/absence table for each individual. (2024-09-26)
Subject	Agricultural Sciences
Keyword	domestication, Indigenous crops, native organisms, population genomics, genomics, cultivation history, cultivation, plant domestication, West Africa
Related Publication	Thomas Kaczmarek, Philippe Cubry, Louis Champion, Sandrine Causse, Marie Couderc, Julie Orjuela, Edak A. Uyoh, Happiness O. Oselebe, Stephen N. Dachi, Charlotte Adje, Emmanuel Sekloka, Enoch G. Achigan-Dako, Abdou R. Ibrahim Bio Yerima, Sani Saidou, Yacoubou Bakasso, Baye M. Diop, Mame C. Gueye, Richard Y. Agyare, Joseph Adjebeng-Danquah, Mathieu Gueye, Jan J. Wieringa, Yves Vigouroux, Claire Billot, Adeline Barnaud and Christian Leclerc. (submitted). Independent domestication and cultivation histories of the two West African indigenous fonio millets crops.
License/Data Use Agreement	CC-BY 4.0

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	all_chr_first_dataset_247samples_FILTERED_masking2DP_RemoveSite05missing.vcf.gz data/Gzip Archive - 1,9 GB Published 4 nov. 2024 0 Downloads MD5: 16774b262b8a351ad35864554d4a4689	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	all_chr_first_dataset_247samples_FILTERED_masking2DP_RemoveSite05missing.vcf.gz.tbi data/Gzip Archive - 442,6 KB Published 4 nov. 2024 0 Downloads MD5: d364cce7e23d43711d6e8452463dd9c0 index of the vcf file	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	all_chr_first_dataset_247samples_FILTERED_masking2DP_RemoveSite05missing_MAF005.vcf.gz data/Gzip Archive - 503,3 MB Published 4 nov. 2024 0 Downloads MD5: 3b29a69918bb20cc82603b90912b884c Principal VCF file used in the study	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	all_chr_first_dataset_247samples_FILTERED_masking2DP_RemoveSite05missing_MAF005.vcf.gz.tbi data/Gzip Archive - 345,6 KB Published 4 nov. 2024 0 Downloads MD5: 4aae91aa248ad062c40770c46196b414 index of of VCF file	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	list247samples.tab data/Tabular Data - 2,7 KB Published 4 nov. 2024 1 Download 1 Variables, 246 Observations UNF:6:Id37Yd1Os2wQVns323wx4g== List of the 247 Digitaria accessions	Preview "data/list247samples.tab" Access File File Access Public Download Options Comma Separated Values (Original File Format) Tab-Delimited RData Download Metadata Variable Metadata Data File Citation EndNote XML RIS BibTeX Explore Options View Data Data Explorer View Data Data Explorer View Data Data Explorer View Data Data Explorer View Data Data Explorer View Data Data Explorer View Data Data Explorer Data Explorer Data Explorer Data Explorer Data Explorer Data Explorer Data Explorer
	output_file.762.bed kmers/PLINK Binary - 59,1 MB Published 4 nov. 2024 0 Downloads MD5: 228fd0a57fb331b5e292ecd6cb85db4c The presence-absence table (bed format)	Access File File Access Public Download Options PLINK Binary Download Metadata Data File Citation EndNote XML RIS BibTeX
	output_file.762.bim kmers/Unknown - 40,1 MB Published 4 nov. 2024 0 Downloads MD5: d5e26dce58d94c313a6772b9a04a4365 List of k-mers (bim format)	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	output_file.762.fam kmers/Unknown - 6,0 KB Published 4 nov. 2024 0 Downloads MD5: 7f57e6f5185e3916c2c552aeb70793de sample information	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	output_file.762.map kmers/Unknown - 36,2 MB Published 4 nov. 2024 0 Downloads MD5: c9fedfcf7cc64a56395afa8e8cf0292a List of k-mers (map format)	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX
	output_file.762.ped kmers/Unknown - 938,4 MB Published 4 nov. 2024 0 Downloads MD5: c4b7407a5d4ad4d669210680eb39edcc presence-absence table of k-mers (ped format)	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18167/DVN1/OYTQO6
Publication Date	2024-11-04
Title	Genomics of white and black fonio millets : passport data, snp and kmer files.
Author	Kaczmarek, Thomas (CIRAD, UMR AGAP Institut, Montpellier) - ORCID: 0000-0001-8526-4651 Cubry, Philippe (IRD, UMR DIADE, Montpellier) Champion, Louis (IRD, UMR DIADE, Montpellier) Causse, Sandrine (CIRAD, UMR AGAP Institut, Montpellier) Couderc, Sandrine (IRD, UMR DIADE, Montpellier) Orjuela, Julie (IRD, UMR DIADE, Montpellier) Uyoh, Edak A. (University of Calabar, Calabar, Nigeria) Oselebe, Happiness O. (Ebonyi State University, Abakaliki, Nigeria) Dachi, Stephen N. (University of Jos, Plateau State, Nigeria) Adje, Charlotte (University of Abomey-Calavi, Cotonou, Republic of Benin) Sekloka, Emmanuel (University of Parakou, Parakou, Republic of Benin) Achigan-Dako, Enoch G. (University of Abomey-Calavi, Cotonou, Republic of Benin) Ibrahim Bio Yerima, Abdou R. (National Institute of Agronomic Research of Niger (INRAN), Niamey, Niger) Saidou, Sani (University of Diffa, Diffa, Niger) Bakasso, Yacoubou (University of Abdou Moumouni, Niamey, Niger) Diop, Baye M. (Institut Sénégalais de Recherches Agricoles (ISRA)) Gueye, Mame C. (Institut Sénégalais de Recherches Agricoles (ISRA)) Agyare, Richard Y. (Council for Scientific and Industrial Research—Savanna Agricultural Research Institute (CSIR-SARI), Ghana) Adjebeng-Danquah, Joseph (Council for Scientific and Industrial Research—Savanna Agricultural Research Institute (CSIR-SARI), Ghana) Gueye, Mathieu (Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal) Wieringa, Jan J. (Naturalis Biodiversity Center, Leiden, the Netherlands.) Vigouroux, Yves (IRD, UMR DIADE, Montpellier) Billot, Claire (CIRAD, UMR AGAP Institut, Montpellier) Barnaud, Adeline (CIRAD, UMR AGAP Institut, Montpellier) Leclerc, Christian (CIRAD, UMR AGAP Institut, Montpellier)
Point of Contact	Use email button above to contact. Kaczmarek, Thomas (CIRAD)
Description	Crop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. In Western Africa, two small indigenous grain cereals are found, black and white fonio (Digitaria exilis and Digitaria iburua respectively). The relationship between these two cultivated crops and wild Digitaria species is still unclear. We analysed whole genome sequences of 265 accessions comprising the two cultivated species and their closely wild relatives. We used different complementary methods and genomic approaches to unravel the domestication history of these fonio millets, which is key to support a process of valorisation of these native species while preserving the diversity necessary for future adaptations. We provide here the passport data, the vcf files, and the kmer files used to perform the analyses. Codes can be accessed in the CIRAD GitLab repository Two compressed VCF files are provided. They contain high quality biallelic SNPs. One is filtered for Minor Allele Frequency (MAF) at 5%. Both vcf.gz are associated to their corresponding index file .tbi Different extensions for the kmer analysis files are provided and correspond to the 1,000,000 k-mer presence/absence table for each individual. (2024-09-26)
Subject	Agricultural Sciences
Keyword	domestication (Agrovoc) http://aims.fao.org/aos/agrovoc/c_2360 Indigenous crops native organisms (Agrovoc) http://aims.fao.org/aos/agrovoc/c_34268 population genomics genomics (Agrovoc) http://aims.fao.org/aos/agrovoc/c_92382 cultivation history cultivation (Agrovoc) http://aims.fao.org/aos/agrovoc/c_2018 plant domestication (Agrovoc) http://aims.fao.org/aos/agrovoc/c_36518 West Africa (Agrovoc) http://aims.fao.org/aos/agrovoc/c_8355
Topic Classification	Génétique et amélioration des plantes (AGRIST-THEMA) https://agrist.cirad.fr/agrist-thema/f-sciences-et-production-vegetales/f30-genetique-et-amelioration-des-plantes
Related Publication	Thomas Kaczmarek, Philippe Cubry, Louis Champion, Sandrine Causse, Marie Couderc, Julie Orjuela, Edak A. Uyoh, Happiness O. Oselebe, Stephen N. Dachi, Charlotte Adje, Emmanuel Sekloka, Enoch G. Achigan-Dako, Abdou R. Ibrahim Bio Yerima, Sani Saidou, Yacoubou Bakasso, Baye M. Diop, Mame C. Gueye, Richard Y. Agyare, Joseph Adjebeng-Danquah, Mathieu Gueye, Jan J. Wieringa, Yves Vigouroux, Claire Billot, Adeline Barnaud and Christian Leclerc. (submitted). Independent domestication and cultivation histories of the two West African indigenous fonio millets crops.
Language	English
Producer	Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) https://www.cirad.fr
Funding Information	WAAPP/PPAAO 2A FAO ANR Agropolis Foundation Horizon H2020: EWA-Belt
Distributor	Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) https://www.cirad.fr
Depositor	Kaczmarek, Thomas
Deposit Date	2024-09-26
Time Period	Start Date: 1977-01-01 ; End Date: 2023-01-01
Date of Collection	Start Date: 1977-01-01 ; End Date: 2023-01-01
Data Type	Dataset; Collection
Software	Cutadapt, Version: 3.1 bwa-mem2, Version: 2.2.1 GATK, Version: 4.2.6.1 vcftools, Version: 0.1.16 iKISS egglib, Version: 3.2.1 Treemix, Version: 1.13 smc++, Version: 1.15.4 fastsimcoal, Version: 2.8 Rstudio, Version: 2023.03.0 Build 386 R, Version: 4.1.2
Related Material	Related codes can be accessed in the CIRAD GitLab repository

Geospatial Metadata

Geographic Coverage	Senegal Mali Burkina Faso Niger Nigeria Guinea Ghana Benin Togo Chad Cameroon Yemen Tanzania, United Republic of Kenya South Sudan Central African Republic

Life Sciences Metadata

Other Organism	Digitaria exilis; Digitaria iburua

Métadonnées CIRAD

Filière(s) Agrist	XA7 Fonio
CTS	CTS 1 - Biodiversité
Data collection method	Experimental data

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