Hawaii Agriculture Research Center

Coffea arabica L. var. 'Kona Typica' is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of 'Kona Typica' using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of 'Kona Typica' provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in cases where known diploid ancestors are absent. In this study, we introduce a novel approach that leverages long terminal repeat retrotransposons (LTR-RTs) coupled with the serial similarity matrix (SSM) method to assign genome assemblies to subgenomes, particularly beneficial for those without known diploid progenitor genomes. The SSM method helps identify subgenome-specific LTRs and facilitates the inference of the timing of allopolyploidization events. We validated the efficacy of the SSM approach using well-studied allopolyploid genomes, Eragrostis tef and Gossypium hirsutum, alongside artificially created allotetraploid genomes, GarGra and GmaGso. Our results demonstrated the robustness of the method and its effectiveness in assigning chromosomes to subgenomes. We then applied the SSM method to the octoploid strawberry genome. Our analysis revealed three allopolyploidization events in the evolutionary trajectory of the octoploid strawberry genome, shedding light on the evolutionary process of the origin of the octoploid strawberry genome and enhancing our understanding of allopolyploidization in this complex species.

Abstract Plant breeding in the public sector is a multigenerational process that creates new plant varieties intended to meet current and future needs of society. Many public sector plant breeding programs are over a century old, and they continue to curate plant genetic resources that are far older still. While individual breeders serve as temporary leaders of these programs and the plant genetic resources they maintain, it is only their institutions that have the capacity to provide the necessary generational glue, enabling the accrual of long‐term value to both breeders and society. Identifying best practices to ensure mutual benefit to both public sector breeders and their institutions is critical to achieving the smooth leadership transitions necessary for the sustainability and long‐term impact of public breeding programs. The findings presented here suggest that the successful passing of the torch in such programs depends not only on strategic institutional support but also, critically, on the routine actions and mindset of the breeders entrusted with their leadership.

Journal Article Making a Modern U.S. West: The Contested Terrain of a Region and Its Borders, 1898–1942 Get access Making a Modern U.S. West: The Contested Terrain of a Region and Its Borders, 1898–1942. By Sarah Deutsch. (Lincoln: University of Nebraska Press, 2022. xii, 640 pp. $50.00.) Heather Fryer Heather Fryer Hakolou, Hawaii Search for other works by this author on: Oxford Academic Google Scholar Journal of American History, Volume 110, Issue 3, December 2023, Pages 572–573, https://doi.org/10.1093/jahist/jaad317 Published: 01 December 2023

Several species of lady(bird) beetles have been purposefully and inadvertently introduced for more than 100 years in the Hawaiian Archipelago. Here, we report new state records for two lady beetle species in Hawai‘i, 20 new island records associated with 14 lady beetle species, and prey information associated with eight records. The update includes new geographic distribution records from five of the eight main islands and the Northwestern Islands of the Hawaiian Archipelago. New state records are reported for Delphastus pallidus LeConte, 1878 and Novius pumilus (Weise, 1892) in Hawai‘i. New island records are reported for Brumoides suturalis (Fabricius, 1798); Cycloneda sanguinea sanguinea Linnaeus, 1763; Diomus roseicollis (Mulsant, 1853); Hyperaspis connectens (Thunberg, 1808); Hyperaspis silvestrii Weise, 1909; Nephaspis bicolor Gordon, 1982; Nephus roepkei (Fluiter, 1938); Psyllobora vigintimaculata (Say, 1824); Rhyzobius lophanthae (Blaisdell, 1892); Scymnobius bilucernarius (Mulsant, 1850); Scymnus (Pullus) latemaculatus Motschulsky, 1858; Serangium maculigerum Blackburn, 1892; an undetermined Pharoscymnus sp. previously recorded in Hawai‘i; and an undetermined Sticholotis sp. previously reported from Hawai‘i. We report Laos as a new country record for the Sticholotis sp. Prey records are documented in Hawai‘i that include Tetraleurodes acaciae (Quaintance, 1900) for D. pallidus; Aleurodicus dispersus Russell, 1965 for S. maculigerum; Bemisia argentifolii Bellows & Perring 1994 and Metaleurodicus cardini (Back, 1912) for N. bicolor; Aleurotrachelus trachoides (Back, 1912) for N. indus and D. roseicollis; Aonidiella orientalis for R. lophanthae; and Aphis nerii Boyer de Fonscolombe, 1841 for S. latemaculatus. The new records demonstrate the value of ongoing sampling and regular examination of undetermined collections.

Food-based baits are an important component of trapping networks designed to detect invasive tephritid fruit flies (Diptera: Tephritidae). An aqueous solution of torula yeast plus borax (TYB) is widely used, but synthetic food lures have been developed to facilitate field procedures, ensure standard composition, and lengthen the interval of bait attractiveness. Cone-shaped dispensers, containing ammonium acetate, putrescine, and trimethylamine (so-called 3C food cones), are currently being used in some large-scale trapping systems (e.g., Florida). Prior work in Hawaii showed that traps baited with 3C food cones capture similar numbers of Mediterranean fruit flies (medflies), Ceratitis capitata (Wiedemann), as TYB-baited traps after 1-2 wk of weathering but capture fewer medflies thereafter. In addition, 3C food cones attract fewer oriental fruit flies, Bactrocera dorsalis (Hendel), and melon flies, Zeugodacuscucurbitae (Coquillett) than TYB even when the food cones are freshly deployed. The current study describes an additional trapping experiment that expands upon earlier work by (i) presenting 3C food cones either unbagged (as done previously) or in nonporous or breathable bags to possibly reduce volatilization and lengthen bait effectiveness and (ii) measuring the content of the 3 components over time to potentially associate fruit fly captures with the loss of these food cone constituents. Implications of these findings for fruit fly surveillance programs are discussed.

La mosca oriental de la fruta, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), es una plaga agrícola mundial que ataca una gran variedad de frutas y verduras de importancia comercial. Muchos países mantienen programas de trampeo para detectar incursiones de esta plaga, y el trampeo depende en gran medida del metil eugenol, un poderoso atrayente para los machos de B. dorsalis, que generalmente se aplica como líquido a una mecha de algodón contenida dentro de las trampas Jackson. Sin embargo, este método requiere mucho tiempo, incurre en una alta volatilidad (pérdida) del señuelo y conlleva riesgos para la salud. Los datos existentes indican que los dispensadores sólidos de metil eugenol son una alternativa viable en vez del uso de señuelos líquidos. Basado en el trabajo de campo en cafetal de Hawái, el presente estudio muestra diferencias no significativas en las capturas de machos de B. dorsalis silvestres en intervalos de 12 semanas entre trampas cebadas con una mecha que contiene 6 ml de metil eugenol líquido recién aplicado y trampas cebadas con una tapón polimérico u oblea que contenía una cantidad similar de metil eugenol. El contenido residual de metil eugenol también se midió para dispensadores sólidos durante el período de exposición a la intemperie, pero su atractivo duradero (≥ 12 semanas) impidió la identificación del nivel umbral del señuelo por debajo del cual los dispensadores sólidos eran ineficaces. Se discuten las implicaciones de estos hallazgos para los programas de trampeo.

Abstract Traditional Hawaiian fishponds, called loko iʻa, are a low‐impact and culturally important aquaculture system that historically produced significant fish yields. To better understand the structure of the contemporary food web of the restored Heʻeia fishpond, a mark‐recapture experiment was conducted to estimate the population abundance of the three dominant predatory fishes, and gut content, genetic barcoding, and stable isotope analyses were used to assess their diets. Great barracuda Sphyraena barracuda had the largest estimated population at 190 individuals, followed by 89 giant trevally Caranx ignobilis and 19 bluefin trevally Caranx melampygus. The three species were caught throughout the pond, with C. ignobilis concentrated in the deeper northwest area near a mangrove island. Diets of the three species consisted mainly of nearshore, estuarine fishes, and crustaceans. Prey taxonomic resolution was greatly improved with the use of genetic barcoding since most fish were too degraded to be visually identified. Trophic level calculations and isotopic niche breadth comparisons indicated that C. ignobilis and S. barracuda occupied similar ecological niches in the fishpond, and stable isotope mixing models revealed that their long‐term diets were mostly comprised glass shrimp (Palaemon sp.), mangrove swimming crab (Thalamita crenata), and an invasive Australian mullet (Osteomugil engeli). The native mullet (Mugil cephalus), a primary food fish species from the fishpond, was not identified in the diets of the predatory fishes in this study nor in a previous diet study decades ago prior to the introduction of Australian mullet. The inclusion of the invasive Australian mullet in the contemporary diets of the predatory fishes demonstrates a shift towards the newly available prey which may benefit the native mullet populations. These findings improve the understanding of food web dynamics in contemporary Hawaiian fishponds and provide an example of native predatory fishes consuming an invasive species as part of their diets.

The sampling intensive mining and environmental industries share a common need for representative data but differ in the motivations to accomplish this objective. The desire to obtain representative sample data for “commodities” in the mining industry is driven by anticipated economic gain and the exploitation of natural resources. The desire to obtain representative sample data for “contaminants” in the environmental industry is driven by anticipated social gain and the protection of natural resources. In terms of obtaining reliably representative data, motivation driven by economic gain has thus far been the clear winner. Theory of Sampling concepts are well established and tested in the mining industry. The environmental industry, in contrast, has traditionally been plagued by scientifically unsound sampling practices and data that are not reliably representative of conditions in the field. This has significant implications for topics ranging from the efficient identification and remediation of contaminated industrial lands to the accurate assessment of risk to human health and the environment. This paper explores the nature and cause of this dichotomy and presents a methodical approach for application of Theory of Sampling concepts to environmental testing of soil, water and air. Much of the problem is tied to a general recognition of compositional and distributional heterogeneity in contaminated media but unawareness of a method to control it or an understanding of the magnitude of potential error. As a result, published regulatory guidance focused on classical sampling and statistical methods appropriate for testing of“finite element” media. A lone exception is testing of indoor air, where concepts of “Decision Units” and sampling methods more appropriate for testing of “infinite element” media have long been employed to control and represent heterogeneity. The solutions are, in hindsight, relatively simple. Pushback from affected parties and even scientists and environmental agencies can be significant, however. This is primarily due to a lack of training of environmental professionals in the Theory of Sampling and the common absence of clear evidence of erroneous or misleading sample data in the field. Reluctance to change is also tied in some cases to implications regarding liability for past and ongoing projects. The need for more reliable, efficient and science-based methods to assess and address risk posed by environmental contamination is clear, however. Progress will be made by countries like China that are beginning to tackle legacies of early development and are able to learn from the successes as well as the mistakes of countries that have been addressing environmental contamination for several decades. Training of environmental workers as well as pressure from liability-savvy responsible parties, attorneys and financial institutions will continue to force the industry to evolve, to the benefit of the environment as well as stakeholders on all sides.