Replication Data for: Complex evolutionary history of coffees including Coffea canephora (Robusta coffee) revealed by full plastid genomes and 28,800 nuclear SNPs analyses

Version 1.0
Guyot, Romain; Charr, Jean-Claude; Garavito, Andrea; Guyeux, Christophe; Crouzillat, Dominique; Descombes, Patrick; Ly, Serigne; Raharimalala, Eva; Rakotomalala, Jean-Jacques; Stoffelen, Piet; Janssen, Steven; Hamon,Perla, 2020, "Replication Data for: Complex evolutionary history of coffees including Coffea canephora (Robusta coffee) revealed by full plastid genomes and 28,800 nuclear SNPs analyses", https://doi.org/10.23708/KWRIJJ, DataSuds, V1
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Description
The dataset concerns all chloroplast complete sequences for Coffea genus. Sequences were annotated with the Genbank format (*.gb). (2020-03-03)
Subject Agricultural Sciences
Keyword Chloroplast, Coffea, Evolution
Notes De novo plastid genome reconstruction was done by mapping raw reads to the C. arabica chloroplast using Bowtie2 (Langmead and Salzberg, 2012), with flags “--very-fast-local” and “--al-conc”. Redundant reads were eliminated using function “clumpify” from the package bbmap (https://github.com/BioInfoTools/BBMap), with the “dedupe” option activated. Finally, the obtained reads were assembled using NOVOPlasty (version 2.7.2) (Dierckxsens, 2017), with a sequence seed corresponding to position 20000 to 20101 to the C. arabica chloroplast. Plastid genomes annotation were done using GeSeq (Tillich et al., 2017).
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1_List_species.csv
Comma Separated Values - 3.0 KB
Published Mar 9, 2020
21 Downloads
MD5: 5fb8ac725eb3871794678ffa40000200
C.arabica-ET39.gb
Chloroplast_genbank/Unknown - 265.7 KB
Published Mar 9, 2020
14 Downloads
MD5: 3ce465dffb2c0fe93f883310496880d7
Data
C.boiviniana-A980.gb
Chloroplast_genbank/Unknown - 265.4 KB
Published Mar 9, 2020
11 Downloads
MD5: 696cc36c958f9b0ad695bbd78a76569b
Data
C.brevipes-C417FL.gb
Chloroplast_genbank/Unknown - 265.3 KB
Published Mar 9, 2020
10 Downloads
MD5: 86b87b10d7a4e540c4aa9e91bbb667c5
Data
C.canephora-BUD15_V1.gb
Chloroplast_genbank/Unknown - 265.6 KB
Published Mar 9, 2020
12 Downloads
MD5: 1099ec4561cf9ba6373db5a0459ac828
Data
C.canephora-C021.gb
Chloroplast_genbank/Unknown - 242.5 KB
Published Mar 9, 2020
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MD5: 2f8960a77fb03be56779ffcd03a90863
Data
C.canephora-C033.gb
Chloroplast_genbank/Unknown - 242.5 KB
Published Mar 9, 2020
10 Downloads
MD5: d166d8a91238c0392524f5830383352c
Data
C.canephora-DH200.gb
Chloroplast_genbank/Unknown - 265.2 KB
Published Mar 9, 2020
10 Downloads
MD5: 0f5e35dbb1ed9d75826ca45a8d87ef36
Data
C.canephora-FRT81.gb
Chloroplast_genbank/Unknown - 265.2 KB
Published Mar 9, 2020
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MD5: 107a64307d20e191ff73bf3eeab81cb9
Data
C.canephora_NC_030053.gb
Chloroplast_genbank/Unknown - 294.3 KB
Published Mar 9, 2020
10 Downloads
MD5: 59f83dea37bcda3e97e8a4caded3ecdd
Data
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