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Backgrounds: Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods: We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P.mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results: The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion: This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics. [ABSTRACT FROM AUTHOR]

Rhododendron is the largest genus in Ericaceae and is well known for its diversity and beauty of flowers present in different species, making it a much‐revered lineage of ornamental plants. Many species of Rhododendron are intolerant of high temperatures, which are becoming more common and intense in urban areas under global climate change. Therefore, the discovery and description of genes from heat‐tolerant Rhododendron lineages are essential in the development of new climate‐resilient cultivars. One such species known to be heat tolerant is Rhododendron × pulchrum Sweet. To better understand the genomics of heat tolerance in this species, we assembled a haplotype‐resolved and chromosome‐scale genome for R. × pulchrum, which had a genome size of 509 Mb; a scaffold N50 of 37 251 370 bp; and contained 35 610 genes. In addition, based on the same reannotation pipeline, we conducted pan‐genomic analyses for all seven available chromosome‐scale Rhododendron genomes and found 14 415 gene groups shared across all species and 18 018 gene groups distributed in the other species, including 1879 gene groups found in only a single species. Finally, we analyzed the transcriptomic data from heat‐treated and non‐heat‐treated R. × pulchrum plants to quantify the genes that are most important during heat stress in an effort to inform the development of climate‐resilient cultivars. This study provides insight into the genome diversity in Rhododendron and targets several genes related to agronomic traits that may help in further analysis. [ABSTRACT FROM AUTHOR]

Bark beetles in the family Curculionidae present a growing hazard to forests worldwide. Like native bark beetles, introduced exotic species can pose a serious threat to North American forests. Ips typographus (Boerner) and Ips sexdentatus (Linnaeus), both native to Europe, are two such pests that have caused widespread forest loss in their native ranges. International trade has led to increased interceptions of Scolytine beetles at ports of entry to the United States. Most intercepted individuals are not identified to species due to lack of expert identifiers, poor specimen quality, or incomplete taxonomy. These same problems affect identification for domestic surveys. Therefore, development of molecular methods for identification of potentially invasive Ips species is essential. Because of the need to scrutinize large numbers of beetles in an efficient manner, we describe a duplex droplet digital PCR (ddPCR) assay to identify I. typographus and I. sexdentatus simultaneously in bulk trap samples containing 500 Scolytinae specimens using a scalable, two-step DNA extraction. This ddPCR method is highly effective for processing the entire contents of beetle traps and identifying these potentially invasive species in a timely and definitive manner. We also describe a nondestructive DNA extraction technique that preserves specimens for morphological identification. Key words: ddPCR, bark beetles, invasive species, bulk sample. Des scolytes de la famille des curculionides constituent une menace grandissante pour les forets partout dans le monde. Comme les scolytes indigenes, les especes exotiques introduites peut representer une menace serieuse pour les forets d'Amerique du Nord. Ips typographus (Boerner) et Ips sexdentatus (Linnaeus), tous deux indigenes en Europe, sont deux de ces ravageurs qui ont cause des pertes en foret, un peu partout dans leur aire naturelle de repartition. Le commerce international a entraine une augmentation du nombre de scolytes interceptes aux points d'entree des Etats-Unis. La plupart des specimens interceptes ne sont pas identifies a l'espece a cause de la penurie de personnel qualifie, de la mauvaise qualite des specimens ou des lacunes de la taxonomie. Le meme probleme existe dans le cas des inventaires domestiques. Par consequent, il est essentiel de developper des methodes moleculaires pour identifier les especes d'Ips potentiellement invasives. Etant donne le besoin d'examiner un grand nombre d'insectes de facon efficace, nous decrivons un essai PCR numerique en gouttelettes (ddPCR) utilise en duplex pour identifier simultanement I. typographus et I. sexdentatus parmi l'ensemble des echantillons dans des pieges contenant 500 specimens de scolytines, en utilisant une methode flexible en deux etapes d'extraction de l'ADN. La methode ddPCR est tres efficace pour traiter tout le contenu des pieges a insectes et pour identifier rapidement et de maniere definitive ces especes potentiellement invasives. Nous decrivons aussi une methode non destructive d'extraction de l'ADN qui permet de preserver les specimens pour une identification morphologique. [Traduit par la Redaction] Mots-cles : ddPCR, scolytes, especes invasives, echantillon global., 1. Introduction Several bark beetles in the family Curculionidae are known for their ability to cause the widespread destruction of forests. Two such species, Ips typographus (Boerner) and Ips sexdentatus [...]

Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future. [ABSTRACT FROM AUTHOR]