Conifer transcriptome assemblies, namely from Abies alba, Abies balsamea and Abies koreana

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Ullrich, Kristian; Roschanski, Anna; Ziegenhagen, Birgit; Liepelt, Sascha; Fady, Bruno, 2024, "Conifer transcriptome assemblies, namely from Abies alba, Abies balsamea and Abies koreana", https://doi.org/10.17617/3.TN2XNM, Edmond, V1

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Description	Conifer transcriptome assemblies, namely from Abies alba, Abies balsamea and Abies koreana
Subject	Biology
Keyword	Abies alba, Abies balsamea, Abies koreana, conifer, transcriptome assembly, gene annotation, transcription factor classification
Related Publication	Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae)https://doi.org/10.3732/apps.1200179
License/Data Use Agreement	CC BY 4.0

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	samples.txt Plain Text - 1.7 KB Published Dec 10, 2024 1 Download MD5: 9da7bf9fd406a819a5293b1e2453b5f7 sample description for Abies alba	Preview "samples.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation EndNote XML RIS BibTeX
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Citation Metadata

Persistent Identifier	doi:10.17617/3.TN2XNM
Publication Date	2024-12-10
Title	Conifer transcriptome assemblies, namely from Abies alba, Abies balsamea and Abies koreana
Author	Ullrich, Kristian Scientific IT group, Max Planck Institute for Evolutionary Biology Roschanski, Anna Experimental Plant Ecology, University of Greifswald Ziegenhagen, Birgit Conservation Biology Group, Philipps University of Marburg Liepelt, Sascha Conservation Biology Group, Philipps University of Marburg Fady, Bruno Ecologie des Forêts Méditerranéennes, INRAE Centre Provence-Alpes-Côte d'Azur
Study Type	other
Description	Conifer transcriptome assemblies, namely from Abies alba, Abies balsamea and Abies koreana
Subject	Biology
Keyword	Abies alba Abies balsamea Abies koreana conifer transcriptome assembly gene annotation transcription factor classification
Topic Classification	transcriptome assembly
Language	English
Funding Information	BiodivERsA: 2012-15 BiodivERsA: 2008-8
Depositor	Ullrich, Kristian
Deposit Date	2024-03-11
Software	Trinity, Software Version: v2.4.0 Trimmomatic, Software Version: v0.36 prinseq-lite, Software Version: v0.20.4 pear, Software Version: v0.9.10 mira, Software Version: v4.9.6 MaSuRCA, Software Version: v3.2.1_08102016 cd-hit, Software Version: v4.6.1 subjunc, Software Version: v1.5.1 picard, Software Version: 2.9.2-SNAPSHOT STAR, Software Version: STAR_2.5.3a_modified Stringtie, Software Version: v1.3.3b cufflinks, Software Version: v2.2.1 GATK, Software Version: 3.8-0-ge9d806836 TransDecoder, Software Version: v5.0.1 PlantTFDB, Software Version: v5.0 OrthoFinder, Software Version: v2.5.5 last, Software Version: v1542 MSA2dist, Software Version: 3.18 phytools, Software Version: v2.1 dplyr, Software Version: v2.4.0 tidyr, Software Version: v1.3.1 ape, Software Version: v5.7 mclust, Software Version: v6.1 feature, Software Version: v1.2.15 compleasm, Software Version: v0.2.5 Embryophyta odb10, Software Version: Embryophyta odb10
Related Publication	Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae) https://doi.org/10.3732/apps.1200179 A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource https://doi.org/10.1534/g3.119.400083 Adaptation to local climate in multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment https://doi.org/10.1038/s41437-019-0240-0
Related Dataset	Abies alba: see related publication; other conifer species: https://bioinformatics.psb.ugent.be/plaza/versions/gymno-plaza/ PLAZA_GYMNO10.pep.all.fa; Abies koreana: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA435847 SRR6781819; Abies balsamea: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA178983 SRR699134; Abies lasiocarpa: https://doi.org/10.1038/s41586-019-1693-2
Geolocation	48.37888889, 8.10333333, GAL1 Black Forest 540 m. a.s.l. 48.37888889, 8.10333333, GAL2 Black Forest 540 m. a.s.l. 48.37888889, 8.10333333, GAL3 Black Forest 540 m. a.s.l. 48.67611111, 8.17055556, HAG1 Black Forest 590 m. a.s.l. 48.67611111, 8.17055556, HAG2 Black Forest 590 m. a.s.l. 48.67611111, 8.17055556, HAG3 Black Forest 590 m. a.s.l. 44.30555556, 5.23777778, s9 Ventoux 1100 m a.s.l. 44.30555556, 5.23777778, s16 Ventoux 1100 m a.s.l. 44.30555556, 5.23777778, s20 Ventoux 1100 m a.s.l. 44.2775, 5.24222222, s26 Ventoux 1350 m a.s.l. 44.2775, 5.24222222, s35* Ventoux 1350 m a.s.l. 44.2775, 5.24222222, s39 Ventoux 1350 m a.s.l.

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