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Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa of Cotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships of Cotinus based on whole cp genomes, protein‐coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113–114 genes were identified in the genomes. Seven non‐coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genes matK and rps8 in the Cotinus cp genomes. Phylogenetic results confirmed that Cotinus is a monophyletic group but the widely distributed species Cotinus coggygria is not monophyletic. The divergence‐time analysis suggested that Cotinus underwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny of Cotinus and related taxa. [ABSTRACT FROM AUTHOR]

The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbc L has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbc L sequences currently available in Gen Bank, we attempted to determine how well a region of rbc L performs as a barcode in species discrimination. We found that the rbc Lb region was more variable than the frequently used rbc La region. Both universal and plant group-specific primers were designed to amplify rbc Lb, and the performance of rbc La and rbc Lb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbc La and from 36.67% to 90.89% for rbc Lb. Successful species discrimination ranged from 5.19% to 96.33% for rbc La and from 22.09% to 98.43% for rbc Lb in species-rich families, and from 0 to 88.73% for rbc La and from 2.04% to 100% for rbc Lb in species-rich genera. Both regions performed better for lower plants than for higher plants, although rbc Lb performed significantly better than rbc La overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbc Lb as a universal plant barcode. [ABSTRACT FROM AUTHOR]

Speciation events often occur with adaptive radiation. The factors that promote these adaptive radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used the adaptive radiated genus Ligustrum to evaluate the relative contributions of the environment, species interactions, phylogenetic diversity, and diversification rates in generating extant species diversity patterns. Using complete chloroplast genome data, we reconstructed the highly supported and dated backbone phylogenetic relationships of Ligustrum. Biogeographic results indicated that Ligustrum originated in Southwest China during the Oligocene and spread to suitable areas that were warm and humid via 18 dispersal events. For the overlapping ranges of species pairs, a smaller phylogenetic distance was detected in high species overlap than in low species overlap, which is consistent with no significant difference in niche among the different species. We found that the phylogenetic diversity and interspecies competition induced by insignificant niche divergence shaped the global pattern of Ligustrum diversity. [ABSTRACT FROM AUTHOR]

Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles. [ABSTRACT FROM AUTHOR]

The smoke tree ( Cotinus coggygria Scop.) is a woody species mainly distributed in the Mediterranean region and East Asia, known for its high ecological and ornamental value. Investigation of changes in suitable habitats under different conditions can provide valuable insights with implications for predicting the distribution of C. coggygria . In this study, we employed a MaxEnt model to simulate the current, historical, and future suitable habitat of C. coggygria using distribution records and environmental variables. The results indicated that climatic variables had a much stronger impact on the suitable habitat of this species compared with soil and topographic variables, and bio11 (mean temperature of the coldest quarter) and bio12 (annual precipitation) played particularly important roles in determining the suitable habitat. The core distribution of C. coggygria exhibited an East Asian-Tethyan disjunction. During the glacial period (Last Glacial Maximum), C. coggygria in Europe was concentrated in the glacial refugia in southern Europe; its range was substantially smaller during the glacial period than during interglacial periods (mid-Holocene). In contrast, C. coggygria in East Asia survived in regions similar to those of the interglacial period. Future climate change led to a gradual northward expansion of suitable habitats for C. coggygria , and the area of suitable habitat was substantially larger in Europe than in East Asia. There were significant differences among the four climate scenarios in Europe, with minimal variation in East Asia. Our findings provide valuable insights into the contrasting effects of climate change on European and East Asian populations of C. coggygria , which enhances our understanding of Eurasian species with discontinuous distributions.

The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the pet A- psb J intergenic region and rpl 16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae., Competing Interests: The authors declare there are no competing interests.