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Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data by Xiang Huang; Yalin Jiao; Jiaxing Guo; Ying Wang; Guangming Chu; Mei Wang is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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Haloxylon ammodendron, a xero-halophytic shrub of Chenopodiaceae, is a dominant species in deserts, which has a strong drought and salt tolerance and plays an important role in sand fixation. However, the codon usage bias (CUB) in H. ammodendron is still unclear at present. In this study, the codon usage patterns of 38,657 coding sequences (CDSs) in the newly released whole-genome sequence data of H. ammodendron and 3,948 CDSs in the previously obtained transcriptome sequencing data were compared and analyzed. The results showed that the CDSs with the total guanine and cytosine (GC) content in the range of 40-45 % was the most in the genome and transcriptome. Among which, the GC1, GC2, and GC3 contents of genomic CDSs were 50.83 %, 40.56 %, and 40.23 %, respectively, and those of CDSs in the transcriptome were 47.16 %, 39.02 %, and 39.59 %, respectively. Therefore, the bases in H. ammodendron were rich in adenine and thymine, and the overall codon usage was biased toward A-and U-ending codons. The analysis of neutrality plot, effective number of codon (ENC) plot, and parity rule 2 (PR2) bias plot showed that both natural selection and mutation pressure had great influences on the C

Who reads Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data?

Author

Xiang Huang; Yalin Jiao; Jiaxing Guo; Ying Wang; Guangming Chu; Mei Wang

Publisher

Elsevier BV

Published

2022

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)