Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model

To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation

Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae

Complete chloroplast genome of Pistacia chinensis Bunge (Anacardiaceae: Rhoideae), an important economical and ornamental plant

Pistacia chinensis Bunge (Anacardiaceae: Rhoideae) is a rare resource plant that originated in China, and has been widely used in horticultural and production field. In this study, we sequenced the complete chloroplast genome of P. chinensis on the Illumina platform by shotgun genome skimming method. The complete chloroplast genome of P. chinensis was 160,596 bp in length with the GC content 37.9%, which was comprised of a large single copy (LSC) region of 88,310 bp, a small single copy (SSC) region of 19,090bp, and a pair of inverted repeats (IRA/IRB) of 26,598 bp. The chloroplast genome encoded 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis constructed using maximum likelihood (ML) method strongly supported the monophyly of each genus used in the family Anacardiaceae, and the genus Pistacia is a sister group to the genus Rhus with 100% bootstrap value. Pistacia chinensis Bunge was sister to P. vera and then grouped with Pistacia weinmaniifolia as a cluster

Detoxification Gene Families at the Genome-Wide Level of <i>Rhus</i> Gall Aphid <i>Schlechtendalia chinensis</i>

The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-S-transferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research

Characterization of the Complete Chloroplast Genome of Rhus Chinensis(Anacardiaceae), An Important Medicinal and Economic Plant from China

International audienceRhus chinensis is a common deciduous tree in the warm temperate zoneof eastern Asia, on which Chinese sumac aphids live to form gallnuts with richtannins. Here, we assembled the complete chloroplast genome of R. chinensiswith the shot-gun genome skimming method on an Illumina HiSeq4000 platform.The complete chloroplast genome of R. chinensis was 149,083 bp in length andhad a standard quadripartite structure with the large (LSC, 97,271 bp) and small(SSC, 18,524 bp) single copy regions separated by a pair of inverted repeats (IRs,16,644 bp each). We successfully annotated 126 genes, including 82 protein-cod-ing genes, 36 tRNAs genes and eight rRNAs genes. Among these genes, 29 geneslocated in IR regions. The overall GC content of the complete chloroplast genomehighly reaches 45.5

Characterization of the Complete Chloroplast Genome of Rhus Chinensis(Anacardiaceae), An Important Medicinal and Economic Plant from China

International audienceRhus chinensis is a common deciduous tree in the warm temperate zoneof eastern Asia, on which Chinese sumac aphids live to form gallnuts with richtannins. Here, we assembled the complete chloroplast genome of R. chinensiswith the shot-gun genome skimming method on an Illumina HiSeq4000 platform.The complete chloroplast genome of R. chinensis was 149,083 bp in length andhad a standard quadripartite structure with the large (LSC, 97,271 bp) and small(SSC, 18,524 bp) single copy regions separated by a pair of inverted repeats (IRs,16,644 bp each). We successfully annotated 126 genes, including 82 protein-cod-ing genes, 36 tRNAs genes and eight rRNAs genes. Among these genes, 29 geneslocated in IR regions. The overall GC content of the complete chloroplast genomehighly reaches 45.5

Closing the Gap: Horizontal Transfer of <i>Mariner</i> Transposons between <i>Rhus</i> Gall Aphids and Other Insects

Horizontal transfer of transposons (HTT) is an essential source of genomic evolution in eukaryotes. The HTT dynamics are well characterized in eukaryotes, including insects; however, there is a considerable gap in knowledge about HTT regarding many eukaryotes’ species. In this study, we analyzed the events of the HTT between Rhus gall aphids (Hemiptera) and other insects. We analyzed the Mariner-like transposable elements (MLEs) belonging to Rhus gall aphids for the possible HT events. The MLEs have a patchy distribution and high similarity over the entire element length with insect MLEs from different orders. We selected representative sequences from the Rhus gall MLEs and identified five events of HT between MLEs of Rhus gall aphids and other insects from five different orders. We also found multiple HTT events among the MLEs of insects from the five orders, demonstrating that these Mariner elements have been involved in recurrent HT between Rhus gall aphids and other insects. Our current study closed the knowledge gap surrounding HTT and reported the events between Rhus gall aphids and other insects for the first time. We believe that this study about HTT events will help us understand the evolution and spread of transposable elements in the genomes of Rhus gall aphids

Data from: A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae)

We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, to investigate putative hybrid origins of O. intermedius, and to provide additional insights on relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively-obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among-species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, P < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them

Additional file 8 of Genome-wide identification and characterization of the chemosensory relative protein genes in Rhus gall aphid Schlechtendalia chinensis

Additional file 8: Table S4. Nucleotide substitution rate of chemoreception gene in Schlechtendalia chinensis