KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

KaKs_Calculator 3.0 is an updated toolkit that is capable for calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate normalized by synonymous substitution rate of adjacent coding sequences. As testified on empirical data, it shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at whole genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation

Motivation The nonsynonymous/synonymous substitution rate ratio (dN/dS) is a commonly used parameter to quantify molecular adaptation in protein-coding data. It is known that the estimation of dN/dS can be biased if some evolutionary processes are ignored. In this concern, common ML methods to estimate dN/dS assume invariable codon frequencies among sites, despite this characteristic is rare in nature, and it could bias the estimation of this parameter. Results Here we studied the influence of variable codon frequencies among genetic regions on the estimation of dN/dS. We explored scenarios varying the number of genetic regions that differ in codon frequencies, the amount of variability of codon frequencies among regions and the nucleotide frequencies at each codon position among regions. We found that ignoring heterogeneous codon frequencies among regions overall leads to underestimation of dN/dS and the bias increases with the level of heterogeneity of codon frequencies. Interestingly, we also found that varying nucleotide frequencies among regions at the first or second codon position leads to underestimation of dN/dS while variation at the third codon position leads to overestimation of dN/dS. Next, we present a methodology to reduce this bias based on the analysis of partitions presenting similar codon frequencies and we applied it to analyze four real datasets. We conclude that accounting for heterogeneous codon frequencies along sequences is required to obtain realistic estimates of molecular adaptation through this relevant evolutionary parameter. Availability and implementation The applied frameworks for the computer simulations of protein-coding data and estimation of molecular adaptation are SGWE and PAML, respectively. Both are publicly available and referenced in the study. Supplementary information Supplementary data are available at Bioinformatics online.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa

The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon–intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa’s strong salinity tolerance.

Population genetic structure and selective pressure on the mitochondrial ATP6 gene of the Japanese sand lance Ammodytes personatus Girard

Thermoregulation has been suggested to influence mitochondrial DNA (mtDNA) evolution. Previous studies revealed that the mitochondrial protein-coding genes of fish living in temperate climates have smaller dN/dS (Non-synonymous substitution rate/Synonymous substitution rate) than tropical species. However, it is unknown whether different geographic populations of one fish species experience stronger selective pressures between cold and warm climates. The biological characteristics of the Japanese sand lance, Ammodytes personatus in the North-western Pacific is well-suited for assessing the performance of mtDNA evolution among separate geographic populations. In this study, we focused on the mitochondrial ATP6 gene of A. personatus using 174 individuals from eight different sea temperature populations. Two distinct haplotype lineages and a significant population structure (P = 0.016) were found in this species. The frequencies of the two lineages varied with the changes of annual sea temperature. The southern lineage (lineage A, dN/dS = 0.0384) showed a larger dN/dS value than the northern lineage (lineage B, dN/dS = 0.0167), suggesting that sea temperature greatly influences the evolution of the two lineages. The result provides robust evidence of local adaptation between populations in A. personatus.

Thermal adaptation of Japanese sand lance (Ammodytes personatus) in different ocean currents revealed by the cytochrome-b gene

To assess the possible thermal selection on mitochondrial coding genes in cold water species, we explored the population structure of Japanese sand lance (Ammodytes personatus) and performed selection tests on the mitochondrial cytochrome-b gene of species, using 174 individuals from eight different sea temperature populations in different ocean currents. Two distinct haplotype lineages were present in this species, and the lineage frequencies varied with changes in sea temperature. The selection tests showed that A. personatus was subject to purifying selection. Populations living in cold climates had a considerably smaller non-synonymous substitution rate/synonymous substitution rate (dN/dS) than those in temperate areas. The efficiency of the electron transfer chain system may be affected by amino acid changes at codons 353 and 371. These findings provide new evidence that temperature may affect the contemporary distribution of mitochondrial DNA clade frequencies in A. personatus.

The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR- coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte)

Both direct repeats (DR) and inverted repeats (IR) are documented in the published plastomes of four Selaginella species indicating the unusual and diverse plastome structure in the family Selaginellaceae. In this study, we newly sequenced complete plastomes of seven species from five main lineages of Selaginellaceae and also re-sequenced three species (S. tamariscina, S. uncinata and S. moellendorffii) to explore the evolutionary trajectory of Selaginellaceae plastomes. Our results showed that the plastomes of Selaginellaceae vary remarkably in size, gene contents, gene order and GC contents. Notably, both DR and IR structure existed in the plastomes of Selaginellaceae with DR structure being an early diverged character. The occurrence of DR structure was right after the Permian-Triassic (P-T) extinction (ca. 246 Ma) and remained in most subgenera of Selaginellaceae, whereas IR structure only reoccurred in the most derived subg. Heterostachys (ca. 23 Ma). The presence of a pair of large repeats psbK-trnQ, together with DR/IR region in S. bisulcata, S. pennata, S. uncinata, and S. hainanensis, could frequently mediate diverse homologous recombination and create approximately equal stoichiometric isomers (IR/DR-coexisting) and subgenomes. High proportion of repeats is presumably responsible for the dynamic IR/DR-coexisting plastomes, which possess a lower synonymous substitution rate (dS) compared with DR-possessing plastomes. We propose that the occurrence of DR structure, together with few repeats, is possibly selected to adapt to the environmental upheaval during the P-T crisis and the IR/DR-coexisting plastomes also reached an equilibrium in plastome organization through highly efficient homologous recombination to maintain stability.Data depositionAll the plastomes were deposited in GenBank under accession numbers MG272483-MG272484, MH598531-MH598537 and MK156800.

How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection framework

First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.