diff --git a/assays/BUSCO_and_Compleasm_db/README.md b/assays/BUSCO_and_Compleasm_db/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..4ed76233eb59b0823fe60c52582fb95fa15ea4fc 100644
--- a/assays/BUSCO_and_Compleasm_db/README.md
+++ b/assays/BUSCO_and_Compleasm_db/README.md
@@ -0,0 +1,2 @@
+# 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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diff --git a/assays/BUSCO_and_Compleasm_db/isa.assay.xlsx b/assays/BUSCO_and_Compleasm_db/isa.assay.xlsx
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diff --git a/assays/Genome_annotations/README.md b/assays/Genome_annotations/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..55d32a7032e271c6cbb8fe46918eda1959c629e0 100644
--- a/assays/Genome_annotations/README.md
+++ b/assays/Genome_annotations/README.md
@@ -0,0 +1,2 @@
+# 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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diff --git a/assays/Genome_annotations/isa.assay.xlsx b/assays/Genome_annotations/isa.assay.xlsx
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diff --git a/assays/Genome_assemblies/README.md b/assays/Genome_assemblies/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..74545f8a367cf473c0973dc3fe9234ad69637aaf 100644
--- a/assays/Genome_assemblies/README.md
+++ b/assays/Genome_assemblies/README.md
@@ -0,0 +1,4 @@
+# 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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diff --git a/assays/Genome_assemblies/isa.assay.xlsx b/assays/Genome_assemblies/isa.assay.xlsx
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diff --git a/assays/Mercator_Bins/README.md b/assays/Mercator_Bins/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..5c06ae82ba5c90e656d33a04db1af71491c0e220 100644
--- a/assays/Mercator_Bins/README.md
+++ b/assays/Mercator_Bins/README.md
@@ -0,0 +1,2 @@
+# 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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diff --git a/assays/Mercator_Bins/isa.assay.xlsx b/assays/Mercator_Bins/isa.assay.xlsx
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diff --git a/assays/Transposable_elements/README.md b/assays/Transposable_elements/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..f5eaaaeea5c4dd5a33cd1ec31c3e89fbab25b7d2 100644
--- a/assays/Transposable_elements/README.md
+++ b/assays/Transposable_elements/README.md
@@ -0,0 +1,2 @@
+# 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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diff --git a/assays/Transposable_elements/isa.assay.xlsx b/assays/Transposable_elements/isa.assay.xlsx
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diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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diff --git a/studies/Camellia_sinensis_pangenome/README.md b/studies/Camellia_sinensis_pangenome/README.md
index 47423b6daabb037099e940aaf21526bd11de81e8..543071305901c94027bb95b67a3efa0eb4aca8f5 100644
--- a/studies/Camellia_sinensis_pangenome/README.md
+++ b/studies/Camellia_sinensis_pangenome/README.md
@@ -1,3 +1,3 @@
-# *Camellia* 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.
+# *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.
diff --git a/studies/Camellia_sinensis_pangenome/isa.study.xlsx b/studies/Camellia_sinensis_pangenome/isa.study.xlsx
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