Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent oppo...Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.展开更多
Asparagine is an efficient nitrogen transport and storage carrier. Asparagine synthesis occurs by the amination of aspartate which is catalyzed by asparagine synthetase(ASN) in plants. Complete genome-wide analysis an...Asparagine is an efficient nitrogen transport and storage carrier. Asparagine synthesis occurs by the amination of aspartate which is catalyzed by asparagine synthetase(ASN) in plants. Complete genome-wide analysis and classifications of the ASN gene family have recently been reported in different plants. However, systematic analysis and expression profiles of these genes have not been performed in apple(Malus domestica). Here, a comprehensive bioinformatics approach was applied to identify MdASNs in apple. Then, plant phylogenetic tree, chromosome location, conserved protein motif, gene structure, and expression pattern of MdASNs were analyzed. Five members were identified and distributed on 4 chromosomes with conserved GATase-7 and ASN domains. Expression analysis indicated that all MdASNs mRNA accumulated at the highest level in reproductive organs, namely flowers or fruits, which may be associated with the redistribution of free amino acids in plant metabolic organs and reservoirs. Additionally, most of Md ASNs were dramatically up-regulated under various nitrogen supplies, especially in the aboveground part. Taken together, MdASNs may be assigned to be responsible for the nitrogen metabolism and asparagine synthesis in apple.展开更多
基金supported by the National Natural Science Foundation of China (31401822)
文摘Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.
基金financially supported by the National Natural Science Foundation of China(31901574 and 31570271)。
文摘Asparagine is an efficient nitrogen transport and storage carrier. Asparagine synthesis occurs by the amination of aspartate which is catalyzed by asparagine synthetase(ASN) in plants. Complete genome-wide analysis and classifications of the ASN gene family have recently been reported in different plants. However, systematic analysis and expression profiles of these genes have not been performed in apple(Malus domestica). Here, a comprehensive bioinformatics approach was applied to identify MdASNs in apple. Then, plant phylogenetic tree, chromosome location, conserved protein motif, gene structure, and expression pattern of MdASNs were analyzed. Five members were identified and distributed on 4 chromosomes with conserved GATase-7 and ASN domains. Expression analysis indicated that all MdASNs mRNA accumulated at the highest level in reproductive organs, namely flowers or fruits, which may be associated with the redistribution of free amino acids in plant metabolic organs and reservoirs. Additionally, most of Md ASNs were dramatically up-regulated under various nitrogen supplies, especially in the aboveground part. Taken together, MdASNs may be assigned to be responsible for the nitrogen metabolism and asparagine synthesis in apple.
