Genome-wide analysis of codon usage bias in four sequenced cotton species

Abstract

Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

“…Similarly, the M gene ENc value in SARS‐CoV‐2 was decreased by an amount of 3 to 5. Genes with low expression levels have high ENc values and more rare codons 32 . The expression of highly biased genes is considered as high 33 .…”

Comprehensive bioinformatic analysis of newly sequencedTurdoides affinismitogenome reveals the persistence of translational efficiency and dominance of NADH dehydrogenase complex-I in electron transport system over Leiothrichidae family

“…Previous studies have found that, U is preferred at the third 287 position specifically when G or C is present in the first two positions. On the contrary, when 288 the first two positions are taken by A or U; C is the 'right choice' (at third position) 38 . Thus, trnI(gat), trnI(gat) and trnQ(ttg), nad2 and trnW(tca), trnA(tgc) and trnN(gtt), trnS2(tga) and 315 trnD(gtc), trnD(gtc) and cox2, atp6 and cox3, nad3 and trnR(tcg), nad4 and trnH(gtg), 316 trnL1(tag) and nad5, nad5 and cob, cob and trnT(tgt), trnT(tgt) and trnP(tgg) (CR1) along 317 with trnP(tgg) and nad6 (Supplementary file 3).…”

“…This parameter measures the competence of codon-anticodon interactions indicating the 174 accuracy of the translational machinery of genes in the absence of preferred codon set 175 information. We calculated the translational efficiency according to the following equation 38 : 176…”

“…The newly sequenced complete mitogenome of T. affinis was compared with other available 244 mitogenomes from the Leiothrichidae family (Table 2). We considered Garrulax 245 anticodon binding energy 38 . Previous studies have found that, U is preferred at the third 287 position specifically when G or C is present in the first two positions.…”

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

“…Another study in four non-grass monocot species also proposed that the G/C ending codons are optimal and that this preference is not likely caused by mutation biases [11]. Nevertheless, a recent study on four cotton species found the pattern that the pyrimidine-enriched codons (especially those ending with T) have higher frequency in the CDSs [12]. Meanwhile, it was also declared that the GC3 (GC content at the 3rd codon position) method was not always suitable for evolutionary comparisons at different scales [13] although CAI is positively correlated with GC3 [11].…”