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Simple Summary: Old World bollworm is a moth species that causes significant damage to a wide range of agricultural crops. This species was once confined to the eastern hemisphere but has recently spread throughout South America and the Caribbean and has the potential to establish in North America. Molecular detection methods for Old World bollworm have been developed to track its spread and rapidly differentiate it from the native sibling species, corn earworm. Currently, droplet digital PCR (ddPCR) is a preferred method for bulk screening as it is highly accurate and tolerant of PCR inhibitors; however, real-time PCR is less expensive and more widely available in molecular labs. Improvements to DNA extraction yield and purity are crucial for real-time PCR assay optimization, but these improvements must be time- and cost-efficient. In this study, we improve upon previously published bulk DNA extraction methods by reducing bench time and costly materials. Our results indicate that the addition of caffeine and RNase A improves DNA extraction, resulting in higher amounts of target DNA in real-time PCR. Such improvements will enable the use of high throughput screening methods across multiple platforms to improve the probability of detection of Old World bollworm. Helicoverpa armigera is among the most problematic agricultural pests worldwide due to its polyphagy and ability to evolve pesticide resistance. Molecular detection methods for H. armigera have been developed to track its spread, as such methods allow for rapid and accurate differentiation from the native sibling species H. zea. Droplet digital PCR (ddPCR) is a preferred method for bulk screening due to its accuracy and tolerance to PCR inhibitors; however, real-time PCR is less expensive and more widely available in molecular labs. Improvements to DNA extraction yield, purity, and throughput are crucial for real-time PCR assay optimization. Bulk DNA extractions have recently been improved to where real-time PCR sensitivity can equal that of ddPCR, but these new methods require significant time and specialized equipment. In this study, we improve upon previously published bulk DNA extraction methods by reducing bench time and materials. Our results indicate that the addition of caffeine and RNase A improves DNA extraction, resulting in lower Cq values during real-time PCR while reducing the processing time and cost per specimen. Such improvements will enable the use of high throughput screening methods across multiple platforms to improve the probability of detection of H. armigera. [ABSTRACT FROM AUTHOR]

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]

The genus Acacia is a crucial source of industrial papermaking and timber, possessing significant economic value. Due to their nitrogen-fixing ability, rapid growth, and high tolerance to stress, Acacia species have become integral to short-term industrial timber forests, particularly in southern China and various other regions worldwide. Nevertheless, comparative genomic analyses of Acacia species remain limited, impeding the development of molecular markers for identifying and distinguishing between distinct Acacia species as well as distinguishing their wood counterparts from other tree species. To address this gap, we generated plastomic sequences from eight species commonly cultivated in Chinese plantation forests and compared them with existing data. Our findings revealed a generally conserved structure and gene content within the plastid genomes of Acacia. Notably, the dN/dS ratio of genes from distinct functional groups varied, particularly between ribosomal proteins and photosynthesis genes. Furthermore, phylogenetic analyses and sequence comparisons suggest that the introduction of Acacia to China may have been less diverse than previously thought or that interspecies introgression has occurred more frequently than previously documented. This study offers a valuable starting point for future research in this area and for improving timber quality through marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Maintaining and planting sustainable forests is fundamental in perpetuating the essential functions of these ecosystems. A central aspect of managing forests for future resilience is the consideration of past migration and evolution of trees using genetic and genomic data to ensure that functionally appropriate diversity is conserved and utilized. In our study, we generated and compared genetic and genomic data from the plastome to better understand phylogeography and molecular evolution in the tree species Populus tremuloides (aspen). With these analyses, we found evidence of divergence and migration between northern and southern sites. Additionally, evidence of deep incomplete plastome sorting across the Salicaceae was found when examining insertion–deletion (indel) sites associated with DNA repair. By examining these indels in plastomic genes with introns across Salicaceae, we found a strong correlation between the abundance of DNA repair with genomic position and transcript abundance. From our findings, we conclude that previously ignored plastomic data are essential in understanding phylogeography and the evolution of key metabolic processes for improved aspen forest planning. Given the propensity of aspen forests to host high levels of biodiversity, rapidly sequester carbon, absorb excess nitrogen, and efficiently regulate snowmelt, improvements to planning and conservation will be highly impactful. [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 [...]

Simple Summary: Most insect species, like most other animal species, host a number of different viruses, and because the number of insect species are so great, the diversity of viruses in insects is expected to be larger than in any other animal lineage. Despite this expectation, few studies are conducted to characterize such viruses and fewer still are carried out to describe the evolutionary dynamics between host and virus. Here we studied a virus that infects an agriculturally important moth species corn earworm (Helicoverpa zea) by comparing host and viral genomes. From this comparison it was found that the virus has incorporated several host genes among which the gene cytosolic serine hydroxymethyltransferase is not known from any other virus and thus may provide a unique study system for better understanding the function of this gene. Additionally, undescribed genes were found in both the virus and host that possess sequences originating from bacteria. Lastly the prevalence of the virus was tested across a broad geographic range and found to be present in nearly all host populations tested. Given these findings, more studies should be initiated to characterize insect viruses for novel molecular interactions with possible uses in gene editing and insect biological control. Insect viruses have been described from numerous lineages, yet patterns of genetic exchange and viral prevalence, which are essential to understanding host–virus coevolution, are rarely studied. In Helicoverpa zea, the virus HzNV-2 can cause deformity of male and female genitalia, resulting in sterility. Using ddPCR, we found that male H. zea with malformed genitalia (agonadal) contained high levels of HzNV-2 DNA, confirming previous work. HzNV-2 was found to be prevalent throughout the United States, at more than twice the rate of the baculovirus HaSNPV, and that it contained several host-acquired DNA sequences. HzNV-2 possesses four recently endogenized lepidopteran genes and several more distantly related genes, including one gene with a bacteria-like sequence found in both host and virus. Among the recently acquired genes is cytosolic serine hydroxymethyltransferase (cSHMT). In nearly all tested H. zea, cSHMT contained a 200 bp transposable element (TE) that was not found in cSHMT of the sister species H. armigera. No other virus has been found with host cSHMT, and the study of this shared copy, including possible interactions, may yield new insights into the function of this gene with possible applications to insect biological control, and gene editing. [ABSTRACT FROM AUTHOR]

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]

Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources. [ABSTRACT FROM AUTHOR]

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan–Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai–Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region. [ABSTRACT FROM AUTHOR]

Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined. We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses. Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods. Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility. These results as well as analyses of non-synonymous and synonymous mutations, indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution. In addition, divergence events within the Lagerstroemia were dated for the first time. Several of the divergence estimates corresponded to well-known Earth history events, such as the reduction in global temperatures at the Eocene/Oligocene boundary. Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders, as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species. [ABSTRACT FROM AUTHOR]

The study of genomic structural evolution associated with accelerated evolutionary rates that result in avoidance of meltdown and increase biodiversity is becoming ever more possible as the number of available plastomes increases. To more comprehensively analyze rate heterogeneity among monocots and within Poaceae, we sequenced plastomes from four Poaceae species, combined them with publicly available data from ~200 plastomes, and conducted comparative analyses to quantify the pattern of rate heterogeneity between different lineages, functional groups, and periods of evolutionary time. We compared structural differences across the Poaceae to quantify how changes in plastome size correspond to different genomic subunits and the evolution of IR–SC junction boundaries. The substitution rates among ancestral Poaceae were inferred to be exceptionally rapid compared to other monocots but slowed after divergence into extant lineages, which could not be sufficiently explained by positive selection. As such, rapid rates in the ancestral lineage leading to Poaceae might be more closely linked to large‐scale structural changes like the loss of ycf1 and ycf2. The total increase in plastome size across Poaceae was positively correlated with the total length of intergenic spacers, tandem repeats, and dispersed repeats as well as large single copy, and inverted repeats (IRs). The continuous evolution of IR–SC junction boundaries was asynchronous with sizes of total genome and subunits across Poaceae. Future work is needed to better understand what factors in ancestral Poaceae evolved to harness such rapid rates of plastome evolution, avoid a mutational meltdown, and escape the stagnation of strong purifying selection as well as if these factors could be utilized to synthetically control rates. Highlights: Extensive sampling covering all monocotyledonous orders and subfamilies of Poaceae to compare different levels of plastome evolutionary rates heterogeneity.Comprehensively revealed the clade‐specific patterns of plastomes size variations among Poaceae subfamilies.Confirmed the distances of genes to IR–SC boundaries were effective for phylogeny, species identification, and maternal tracing of Poaceae species. [ABSTRACT FROM AUTHOR]

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea , ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices. [ABSTRACT FROM AUTHOR]

The moth species Phthorimaea absoluta (Meyrick) (formerly Tuta absoluta) is serious threat to tomato and other Solanaceous crops worldwide and is invasive throughout Europe, Asia, and Africa. While P. absoluta has not yet been found in the U.S. recent detections in the Caribbean have raised concerns that the species could be introduced to mainland North America. To improve detection capacity, a droplet digital PCR (ddPCR) assay was developed that employs a nondestructive bulk DNA extraction method able to detect one P. absoluta sample among 200 nontargets. Such high-throughput and sensitive molecular assays are essential to preventing introductions through early detection and response. This assay can also be used in areas where P. absoluta is established to monitor outbreaks and track migratory patterns. [ABSTRACT FROM AUTHOR]

DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species. [ABSTRACT FROM AUTHOR]

Globalized trade has resulted in the incidental translocation of numerous insect species, some of which have become invasive in their expanded ranges. While rigorous inspection programs are a regular part of commodity importation, rarely if ever are the internal contents of intercepted insects examined. As part of a genetic diversity project on intercepted Diabrotica undecimpunctata beetles, we detected CO1 DNA that closely matched sequences from Centistes parasitoid wasps in 9% of our samples. The presence of internal parasitoids was confirmed through dissections and imaging, wherein the samples were morphologically consistent with Centistes larvae. Such a discovery suggests that insect translocation as part of trade can be more diverse than initially thought. The case of Centistes in imported Diabrotica may present a positive benefit specifically to agroecosystems through the biological control of pest beetles like Diabrotica. However, drawbacks from such introductions include off-target parasitism of non-pest beetles and resultant impacts to insect populations in undisturbed ecosystems. Thus, examination of intercepted insects beyond the initial species identification is warranted to better understand the potential impacts of human mediated insect translocations. Methods employing high-throughput sequencing and metabarcoding are well suited for such broad-scale identification projects where Diabrotica would be an excellent candidate for this work. [ABSTRACT FROM AUTHOR]

Summary: Carnation (Dianthus caryophyllus) is one of the most popular ornamental flowers in the world. Although numerous studies on carnations exist, the underlying mechanisms of flower color, fragrance, and the formation of double flowers remain unknown. Here, we employed an integrated multi‐omics approach to elucidate the genetic and biochemical pathways underlying the most important ornamental features of carnation flowers. First, we assembled a high‐quality chromosome‐scale genome (636 Mb with contig N50 as 14.67 Mb) of D. caryophyllus, the 'Scarlet Queen'. Next, a series of metabolomic datasets was generated with a variety of instrumentation types from different parts of the flower at multiple stages of development to assess spatial and temporal differences in the accumulation of pigment and volatile compounds. Finally, transcriptomic data were generated to link genomic, biochemical, and morphological patterns to propose a set of pathways by which ornamental traits such as petal coloration, double flowers, and fragrance production are formed. Among them, the transcription factors bHLHs, MYBs, and a WRKY44 homolog are proposed to be important in controlling petal color patterning and genes such as coniferyl alcohol acetyltransferase and eugenol synthase are involved in the synthesis of eugenol. The integrated dataset of genomics, transcriptomics, and metabolomics presented herein provides an important foundation for understanding the underlying pathways of flower development and coloration, which in turn can be used for selective breeding and gene editing for the development of novel carnation cultivars. [ABSTRACT FROM AUTHOR]

The genus Dalbergia contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade, CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) has listed the entire genus in appendix II and the species Dalbergia nigra in appendix I because species in this genus are considered at risk of extinction. Given this, and the fact that species or even genus level determination is nearly impossible from cut timber morphology, alternative molecular methods are needed to identify and track intercepted rosewood. To better identify rosewood using molecular methods, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses, numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis based on the CDS from 77 chloroplast genes, the groups Siam rosewood and scented rosewood resolved as monophyletic, supporting the morphological traits used to delimit these species. In addition, several instances of paraphyly and polyphyly resulting from mismatches between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species, including those frequently intercepted in illegal trade. [ABSTRACT FROM AUTHOR]

Vatica mangachapoi is a tropical tree species native to Southeast Asia. It has long been valued as a timber species because the wood resists decay, but it is now considered vulnerable to extinction due to habitat loss and overexploitation. Here, we present the first chromosome-level genome assembly of V. mangachapo i that we created by combining data from PacBio long read sequencing with Hi-C proximity ligation and Illumina short-read sequencing. The assembled genome was 456.21 Mb, containing 11 chromosome and a BUSCO score of 93.4%. From the newly assembled genome, 46,811 protein-coding genes were predicted. Repetitive DNA accounted for 53% of the genome. Phylogenomic and gene family analyses showed that V. mangachapoi diverged from a common ancestor of Gossypium raimondii 70 million years ago. Transcriptome analyses found 227 genes that were differentially expressed in the leaves of plants grown in normal soil relative to plants grown in dry, coastal, sandy soil. For these genes, we identified three significantly enriched with GO terms: responses to organonitrogen compounds, chitin-triggered immunity, and wound response. This genome provides an important comparative benchmark not only for future conservation work on V. mangachapoi but also for phylogenomics work on Dipterocarpaceae. [ABSTRACT FROM AUTHOR]

Changes in plant leaf color during development are directly related to the accumulation or degradation of certain phytochemicals such as anthocyanins. Since some anthocyanins can be beneficial to human health and provide insights into the biology of leaves, the underlying processes and timing by which plants produce these molecules has been the focus of numerous studies. The tree species Hopea hainanensis generally produces green leaves at all growth stages; however, a few explored individuals have been identified possessing red leaves on the top of the seedlings at a young stage. While the phenomenon of leaf color varying with age has been studied in several species, the underlying mechanisms are largely unknown in H. hainanensis. Using a metabolomics approach, the young red leaves in H. hainanensis were found to contain higher levels of anthocyanins and flavonoids than the young green-leaved individuals. Among anthocyanins, pelargonidin and cyanidin were the most likely candidates contributing to the red color of the young leaves. Transcriptome results indicated the genes related to the production of these anthocyanins were significantly upregulated, leading to greater accumulation of red pigments. Specifically, the expression of several MYB and bHLH genes in young red leaf lines was significantly higher than that in the young green leaf lines, especially HhMYB66 , HhMYB91 , HhMYB6 , and HhbHLH70. As such these four transcription factors are probably the main regulatory genes resulting in young red leaves in H. hainanensis. From these results, comparative analyses with other species can be made to better understand the evolution of pigment biosynthesis and how anthocyanins function in plant metabolism and evolution/adaptation. [ABSTRACT FROM AUTHOR]

Since the endosymbiont origin from α‐Proteobacteria, mitochondrial genomes have undergone extremely divergent evolutionary trajectories among eukaryotic lineages. Compared with the relatively compact and conserved animal mitochondrial genomes, plant mitochondrial genomes have many unique features, especially their large and complex genomic arrangements. The sizes of fully sequenced plant mitochondrial genomes span over a 100‐fold range from 66 kb in Viscum scurruloideum to 11 000 kb in Silene conica. In addition to the typical circular structure, some species of plants also possess linear, and even multichromosomal, architectures. In contrast with the thousands of fully sequenced animal mitochondrial genomes and plant plastid genomes, only around 200 fully sequenced land plant mitochondrial genomes have been published, with many being only draft assemblies. In this review, we summarize some of the known novel characteristics found in plant mitochondrial genomes, with special emphasis on multichromosomal structures described in recent publications. Finally, we discuss the future prospects for studying the inheritance patterns of multichromosomal plant mitochondria and examining architectural variation at different levels of taxonomic organization—including at the population level. [ABSTRACT FROM AUTHOR]

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts. [ABSTRACT FROM AUTHOR]

The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high‐resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise FST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF‐seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range. [ABSTRACT FROM AUTHOR]

The Old World bollworm, Helicoverpa armigera (Hübner), is one of the most destructive agricultural pests worldwide. It was first recorded in Brazil in 2013, yet despite this recent introduction, H. armigera has spread throughout much of Latin America. Where H. armigera has become established, it is displacing or hybridizing with the congeneric New World pest Helicoverpa zea. In addition to the adaptive qualities that make H. armigera a megapest, such as broad range pesticide resistance, the spread of H. armigera in the New World may have been hastened by multiple introductions into South America and/or the Caribbean. The recent expansion of the range of H. armigera into the New World is analyzed herein using mtDNA of samples from South America, the Caribbean Basin, and the Florida Peninsula. Phylogeographic analyses reveal that several haplotypes are nearly ubiquitous throughout the New World and native range of H. armigera , but several haplotypes have limited geographic distribution from which a secondary introduction with Euro-African origins into the New World is inferred. In addition, host–haplotype correlations were analyzed to see whether haplotypes might be restricted to certain crops. No specialization was found; however, some haplotypes had a broader host range than others. These results suggest that the dispersal of H. armigera in the New World is occurring from both natural migration and human-mediated introductions. As such, both means of introduction should be monitored to prevent the spread of H. armigera into areas such as the United States, Mexico, and Canada, where it is not yet established. [ABSTRACT FROM AUTHOR]