ABSTRACT
Objective::To determine the chloroplast genomes of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang, analyze their sequence characteristics and complete the screening of specific DNA barcodes. Method::The chloroplast genomes of L. spicata var. prolifera, O. japonicus in Sichuan and Zhejiang were sequenced, spliced and annotated through high-throughtput sequencing technology, and the structural characteristics and phylogenetic relationships of chloroplast genomes were analyzed by bioinformatics. Result::The total length of chloroplast genome of L. spicata var. prolifera was 155 998 bp, the total content of guanine and cytosine (GC) was 37.7%, and 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes were successfully annotated, a total of 274 simple sequence repeats (SSRs) were detected, the number of codons encoding leucine was the most, while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of O. japonicus in Sichuan province was 156 078 bp, the total content of GC was 37.8%, and 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were successfully annotated, a total of 265 SSRs were detected, the number of codons encoding leucine was the most, while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of O. japonicus in Zhejiang province was 156 207 bp, the total content of GC was 37.7%, and 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were successfully annotated, a total of 274 SSRs were detected with the highest number of codons encoding leucine and the lowest number of codons encoding tryptophan. Conclusion::The phylogenetic trees show that compared with O. japonicus in Sichuan province, L. spicata var. prolifera is more closely related to O. japonicus in Zhejiang province. The variation of non-coding regions of L. spicata var. prolifera, O. japonicus in Zhejiang and Sichuan is greater than that in the coding region. The entire chloroplast genome can be used as a super barcode for identifying species of Ophiopogon and Liriope.
ABSTRACT
<p><b>OBJECTIVE</b>This study investigated the association between a missense SNP in the codon of ADD1 phosphorylation site and the susceptibility of non-cardia gastric cancer in a Chinese population.</p><p><b>METHODS</b>PhosphoSitePlus and dbSNP database were combined to discover missense SNPs in the codon of phosphorylation site. Then, we genotyped the missense SNP in 1, 998 cases with non-cardia gastric cancer and 2, 008 cancer-free controls of Chinese descent. Analysis was conducted by using Logistic model adjusted by gender and age.</p><p><b>RESULTS</b>The rs4963 in the codon of ADD1 phosphorylation site was found. The frequencies of the 3 rs4963 genotypes, CC, CG, GG, among controls were 25.2%, 50.4%, and 24.4%, respectively, among patients were 20.1%, 50.6%, and 29.3%, respectively. Compared with CC genotype, the rs4963 CG genotype and GG genotype significantly increased the risk of non-cardia gastric cancer with the odds ratios being 1.24 (95%CI: 1.06 ∼ 1.46, P = 0.008) and 1.49 (95%CI: 1.25 ∼ 1.78, P < 0.001), respectively.</p><p><b>CONCLUSIONS</b>Fnnctional polymorphism in the phosphorylation site of ADD1 (rs4963) may influence the susceptibility of non-cardia gastric cancer.</p>