Chromosomal Mapping and Duplication Analysis of Cassava AMT2 Genes

The MeAMT2 genes were mapped to the chromosomes utilizing TBtools software (Chen et al., 2020 (link)) according to the information obtained from the cassava genome database. Simultaneously, gene duplication of MeAMT2 genes was analyzed utilizing MCScanX software (Wang et al., 2012 (link)) and illustrated with TBtools. The nucleotide substitution parameters Ks (synonymous) and Ka (non-synonymous) of the duplicated genes were assessed using TBtools, and then the Ka/Ks ratio was calculated. In addition, the gene duplication information from cassava, soybean, and A. thaliana was analyzed using MCscanX software, followed by integral visualization of synteny with TBtools software (Wang et al., 2012 (link); Chen et al., 2020 (link)).

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Xia J., Wang Y., Zhang T., Pan C., Ji Y., Zhou Y, & Jiang X. (2023). Genome-wide identification, expression profiling, and functional analysis of ammonium transporter 2 (AMT2) gene family in cassava (Manihot esculenta crantz). Frontiers in Genetics, 14, 1145735.

Publication 2023

Cassava Chromosomes Duplicated genes Gene duplication Genes Genome Nucleotide Soybean Synteny

Corresponding Organization : Hainan University

Other organizations : Anyang Academy of Agricultural Sciences

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Variable analysis

independent variables

Chromosomal mapping of MeAMT2 genes using TBtools software
Gene duplication analysis of MeAMT2 genes using MCScanX software
Nucleotide substitution parameter (Ks and Ka) analysis of duplicated genes using TBtools
Synteny analysis of gene duplication information from cassava, soybean, and A. thaliana using MCScanX and TBtools

dependent variables

Chromosomal locations of MeAMT2 genes
Presence and patterns of gene duplication for MeAMT2 genes
Nucleotide substitution parameters (Ks and Ka) of duplicated genes
Syntenic relationships of gene duplication events across cassava, soybean, and A. thaliana

control variables

Information obtained from the cassava genome database

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