Genome Assembly and Annotation of Astragalus membranaceus (Fisch.) Bge (AM)

Astragalus membranaceus (AM) is a medicinal herb from the Leguminosae-family. Its dried roots, known as Astragali Radix, possess hepatoprotective, diuretic, tonic, and expectorant activities. They are involved in various functions in Chinese medicine such as anti-aging, anti-tumor, anti-neurodegeneration, regulating blood glucose, and enhancing immunity.Amem.genome.fasta.gz: genome assemlyAmem.gff3.gz: gene structruerepeat.gff.gz: repeat annotationAmem.gene.function.xls: protein functionAM.snp.vcf.gz: Utilizing Astragalus membranaceus (AM) as the reference, a genome alignment with the Astragalus mongholicus (AMM, downloaded from http://www.gpgenome.com/species/109) assemblies was conducted using the NUCmer program from MUMmer4 suite, version 4.0.0. The alignment was performed with specific parameter settings aimed at optimizing match quality: <code>--mum -g 1000 -c 90 -l 40</code>. Subsequently, the delta-filter program was employed to refine the alignment, extracting contiguous blocks with the parameters <code>-1 -l 5000</code>. To identify single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), the show-snps program was applied with the following settings: <code>-Clr -x 1 -T</code>. This report presents the findings pertaining to SNPs.AM.indel.vcf.gz：Utilizing Astragalus membranaceus (AM) as the reference, a genome alignment with the Astragalus mongholicus (AMM, downloaded from http://www.gpgenome.com/species/109) assemblies was conducted using the NUCmer program from MUMmer4 suite, version 4.0.0. The alignment was performed with specific parameter settings aimed at optimizing match quality: <code>--mum -g 1000 -c 90 -l 40</code>. Subsequently, the delta-filter program was employed to refine the alignment, extracting contiguous blocks with the parameters <code>-1 -l 5000</code>. To identify single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), the show-snps program was applied with the following settings: <code>-Clr -x 1 -T</code>. This report presents the findings pertaining to InDels.<br>