Complete Plastid Genome Sequences of Three Tropical African Beilschmiediineae Trees (Lauraceae: Crytocaryeae)

Millions of years of isolation have given Madagascar a unique flora that still reflects some of its relationship with the continents of Africa and India. Here, the complete chloroplast sequence of Beilschmiedia moratii, a tropical tree in Madagascar, was determined. The plastome, with a length of 158,410 bp, was 143 bp and 187 bp smaller than those of two closely related species, B. pierreana and Potameia microphylla, in sub-Saharan Africa and Madagascar with published sequences, respectively. A total of 124 repeats and 114 simple sequence repeats (SSRs) were detected in the plastome of B. moratii. Six highly variable regions, including ndhF, ndhF-rpl32, trnC-petN, pebE-petL, rpl32-trnL, and ycf1, among the three African species were identified and 1151 mutation events, including 14 SVs, 351 indels, and 786 substitutions, were accurately located. There were 634 mutation events between B. moratii and P. microphylla with a mean nucleotide variability (π) value of 0.00279, while there were 827 mutation events between B. moratii and B. pierreana with a mean π value of 0.00385. The Ka/Ks ratios of 86 protein-coding genes in the three African species were less than 1, and the mean value between B. moratii and P. microphylla was 0.184, while the mean value between B. moratii and B. pierreana was 0.286. In this study, the plastid genomes of the three African Beilschmiediineae species were compared for the first time and revealed that B. moratii and P. microphylla from Madagascar were relatively conserved, with low mutation rates and slower evolutionary rates

Comparative Analyses of 18 Complete Chloroplast Genomes from Eleven <i>Mangifera</i> Species (Anacardiaceae): Sequence Characteristics and Phylogenomics

Mangifera plants are tropical fruits that have high economic value and scientific utility. However, the chloroplast genome characteristics and phylogenetic relationships among Mangifera species remain unclear. In this work, we reconstructed maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees using 11 newly sequenced chloroplast genomes as well as six existing genomes obtained from the National Center for Biotechnology Information (NCBI) database. The chloroplast genomes all had a typical quadripartite structure, with lengths ranging from 157,368 to 158,942 bp. The GC-content in the genomes ranged from 37.8% to 37.9%. We found conserved boundaries comprised of two inverted repeats (IRs), large single-copy (LSC) regions, and small single-copy (SSC) regions. Nucleotide polymorphism analysis revealed three hypervariable regions (ycf4-cemA, rps18-rpl20, and rpl32-ndhF) in the LSC and SSC regions, which could potentially be used as DNA barcodes for Mangifera species. According to our phylogenetic analysis, Mangifera plants were clustered into three clades. Among them, all five samples of M. indica formed a monophyletic group in Clade Ⅰ. Clade Ⅱ included seven Mangifera species and could be further divided into five subclades with 100% branch support values. Clade Ⅲ included two M. persiciforma samples that formed a monophyletic group. Taken together, these results provide a theoretical basis for species determination, in addition to shedding light on the evolution of Mangifera

Characteristics of the Complete Chloroplast Genome of Pourthiaea (Rosaceae) and Its Comparative Analysis

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159&ndash;160,401 bp, in which the large single copy was 88,047&ndash;88,359 bp, the small single copy was 19,234&ndash;19,338 bp, and the lengths of a pair of inverted repeats were 26,341&ndash;26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi &gt; 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea

Characteristics of the Complete Chloroplast Genome of <i>Pourthiaea</i> (Rosaceae) and Its Comparative Analysis

Pourthiaea is of great ornamental value because it produces white flowers in spring and summer, red fruit in autumn, and their fruit does not fall in winter. In order to explore the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea, comparative genomics analysis and phylogenetic analysis were conducted using ten published chloroplast genomes of Pourthiaea from the NCBI database. The results showed that the chloroplast genomes of the ten species of Pourthiaea showed typical circular tetrad structures, and the genome sizes were all within the range of 160,159–160,401 bp, in which the large single copy was 88,047–88,359 bp, the small single copy was 19,234–19,338 bp, and the lengths of a pair of inverted repeats were 26,341–26,401 bp. The GC contents ranged from 36.5% to 36.6%. A total of 1017 SSR loci were identified from the chloroplast genomes of the ten species of Pourthiaea, including six types of nucleotide repeats. The gene types and gene distribution of the IR boundary regions of the chloroplast genomes of different species of Pourthiaea were highly conservative, with little variation. Through the sequence alignment of chloroplast genomes, it was found that the chloroplast genomes of the ten species of Pourthiaea were generally highly conservative. The variation mainly occurred in the spacer regions of adjacent genes. Through nucleic acid diversity analysis, three hypervariable regions were screened at Pi > 0.006, namely trnQ(UUC)-psbk-psbl, accD-psal, and ndhF-rpl32-trnL (UAG). Phylogenetic analysis showed that the ten species of the genus Pourthiaea were clustered in the same branch and formed sister groups with the genus Stranvaesia, and that the support rate for the monophyly of the genus Pourthiaea was high. This study can serve as a reference for the breeding, genetic evolution, and phylogeny of Pourthiaea

Firing synchronization and temporal order in noisy neuronal networks

Noise-induced complete synchronization and frequency synchronization in coupled spiking and bursting neurons are studied firstly. The effects of noise and coupling are discussed. It is found that bursting neurons are easier to achieve firing synchronization than spiking ones, which means that bursting activities are more important for information transfer in neuronal networks. Secondly, the effects of noise on firing synchronization in a noisy map neuronal network are presented. Noise-induced synchronization and temporal order are investigated by means of the firing rate function and the order index. Firing synchronization and temporal order of excitatory neurons can be greatly enhanced by subthreshold stimuli with resonance frequency. Finally, it is concluded that random perturbations play an important role in firing activities and temporal order in neuronal networks