README.md

@@ -8,12 +8,11 @@ Pan‐genomes aim to address the presence-absence and copy number variation as w
 
 ## Data Files
 
-[Genome annotations](https://git.nfdi4plants.org/usadellab/Camellia_sinensis_genomics/-/tree/master/assays/Genome_annotations)
+[Genome annotations](https://git.nfdi4plants.org/usadellab/camellia_sinensis_genomics/-/tree/main/assays/Genome_annotations)
 
-[Genome assemblies](https://git.nfdi4plants.org/usadellab/Camellia_sinensis_genomics/-/tree/master/assays/Genome_assemblies)
-
-[Transposable elements](https://git.nfdi4plants.org/usadellab/Camellia_sinensis_genomics/-/tree/master/assays/Transposable_elements)
+[Genome assemblies](https://git.nfdi4plants.org/usadellab/camellia_sinensis_genomics/-/tree/main/assays/Genome_assemblies)
 
+[Transposable elements](https://git.nfdi4plants.org/usadellab/camellia_sinensis_genomics/-/tree/main/assays/Transposable_elements)
 ## Citation
 Tariq, A., Meng, M., Jiang, X., Bolger, A., Beier, S., Buchmann, J.P., Fernie, A.R., Wen, W. and Usadel, B. (2024), In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis. Plant J. [https://doi.org/10.1111/tpj.16874](https://doi.org/10.1111/tpj.16874)
 

assays/BUSCO_and_Compleasm_db/README.md

+# Orthologs database
+These are the eudicots_odb10 databases that were used for the [BUSCO](https://busco.ezlab.org/) and [Compleasm](https://github.com/huangnengCSU/compleasm) analysis.
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assays/Genome_annotations/README.md

+# Genome Annotations
+The combination of ab initio gene prediction using the deep learning tool  [Helixer](https://github.com/weberlab-hhu/Helixer) and the RNASeq-based [StringTie](https://ccb.jhu.edu/software/stringtie/) predicted transcripts were combined with a high-quality genome annotation with [Mikado](https://mikado.readthedocs.io/en/stable/) to select the best transcript sets.
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assays/Genome_assemblies/README.md

+# Genome assembly
+The genome of Anjibaicha, Zijuan, and L618 was initially assembled using [Hifiasm](https://www.nature.com/articles/s41592-020-01056-5) ([v0.19.5] and then purge the assembly using [Purge Haplotigs](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/).
+We only had [Hi-C](https://en.wikipedia.org/wiki/Hi-C_(genomic_analysis_technique)) data for Anjibaicha. First, the Hi-C reads were processed using [Arima pipeline](https://github.com/ArimaGenomics/mapping_pipeline) and then removed small contigs which were highly similar to large scaffolds using [Purge Haplotigs](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/).
+We didn't have Hi-C data for ZJ and L618, so we used [RagTag](https://github.com/malonge/RagTag) using the AJ chromosome as a reference.
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assays/Mercator_Bins/README.md

+# Functional annotation
+The functional annotation for all accession's proteome was performed using [Mercator4](https://www.plabipd.de/mercator_main.html)
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assays/Transposable_elements/README.md

+# Transposable Elements (TEs) annotation
+The advanced Extensive de novo TE Annotator [EDTA](https://github.com/oushujun/EDTA) to identify TEs within the tea genomes. The LTR, TIR, and Helitron modes were run separately, followed by a final EDTA run with `-overwrite 0` and `--cds` options using Mikado's gene model CDS sequence, ensuring accurate and comprehensive annotation of TEs. For pan TE identification, the panEDTA module was used
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studies/Camellia_sinensis_pangenome/README.md

+# *Camellia sinensis* genomes
+
+De novo genome assemblies of 3 diverse tea accessions, the purple-leaved *assamica* cultivar “Zijuan”, the temperature-sensitive *sinensis* cultivar “Anjibaicha” and the wild accession “L618” were merged with eight existing *Camellia* genomes to generate a new pan genome. To obtain leaf material for the de novo assemblies, plants were grown in the tea germplasm resource nursery of Huazhong Agricultural University, Wuhan, China.