In comparison to mitochondrial genomes from other members of the Ericaceae, this assembly is similar to that of Vaccinium macrocarpon at 459 678 bp but considerably smaller than that of the saprophytic Hypopitys monotropa or Rhododendron simsii .Our assembly is the first sequenced genome in the genus Arctostaphylos, representing the initial step toward understanding genetics and adaptation in this highly diversified genus. In addition to enhancing ongoing phylogenetic and conservation research, this assembly will enable investigations of the genetic basis of adaptations including drought tolerance and fire resilience. These traits, which are ecological hallmarks of manzanitas, are of growing importance in the context of the increased drought and fire frequency and intensity that are occurring in California as a result of climate change. This assembly can also serve as a reference for studying the diversification and population genetics of Arctostaphylos, which may shed light on aspects of diversification in other complex groups of the CFP. Arctostaphylos is the third genus with a genome assembly in the heath family, Ericaceae, following release of assembled genome sequences of Rhododendron and Vaccinium . These two genera are of significant economic importance: many species, hybrids, and cultivars of Rhododendron, including rhododendron and azalea, are important landscape and ornamental plants, and the fruits of many Vaccinium species, container raspberries which include cranberry, blueberry, and huckleberry, are consumed by humans and other animals. Species in the Ericaceae are also notable for their ability to tolerate acidic and nutrient-poor soils that often characterize boreal forests and bogs, allowing them to thrive in habitats that are inaccessible to most species.

Their tolerance for these conditions is due in part to the formation of mutualistic associations between the roots of the plants and soil fungi of a type unique to the heath family known as ericoid mycorrhizae. Ericoid mycorrhizae are distinct from common mycorrhizal associations found in most angiosperms, and are far less well understood . Complete genome sequences from three genera in this family will provide a strong foundation for investigating the basis of this unique mutualism and its ability to promote survival in inhospitable soils. The size of the A. glauca assembly is 547Mb, which is similar to the two Rhododendron genomes and half that of V corymbosum, which is tetraploid . The tetraploid nature of V. corymbosum also explains the vastly greater number of duplicated genes in its assembly compared to the two diploid assemblies. The scaffold N50 of the A. glauca assembly is longer than R. williamsianum, and close to R. simsii and V. corymbosum, suggesting that the contiguity of Arctostaphylos is comparable to the other taxa . Analysis using RepeatModeler indicated that 57.71% of the A. glauca genome is composed of different categories of repetitive elements . In contrast, analysis using RepeatModeler identified only 26%, 47.5%, and 44.3% of the genome comprising repeat elements in R. williamsianum, R. simsii, and V. corymbosum respectively. The BUSCO completeness assessment of the A. glauca assembly is higher than R. williamsianum and close to the V. corymbosum , indicating that our final assembly is high quality . Overall, the A. glauca, R. simsii and V. corymbosum genomes are of comparably high contiguity and completeness. The lower contiguity and completeness of the R. williamsianum genome may be due to the lack of HiFi or other longread data in the assembly. This explanation is consistent with other studies demonstrating improved assembly with the inclusion of longer reads . Although the big berry manzanita is a common and widespread species, nearly half of the 60+ manzanita species are rare or threatened.

Many are now represented by only one or two populations, and are thus vulnerable to complete eradication by the increasingly common and intense wildfires experienced across California each year. Our manzanita genome sequence will help fulfill the overall goal of the CCGP, serving as a key resource to assess genetic diversity in these threatened endemics and move forward with coordinated conservation programs.The increasing number of diversified small-scale farms and outdoor-raised livestock in the United States , reflects growing consumer interest and demand for sustainably-produced or organic local foods, including animal products such as meat and eggs. However, there is a lack of research evaluating the unique agricultural management practices of DSSF and if these types of farming operations involve risk factors that affect the transmission of food borne pathogens in the food supply. California is the top agricultural production state in the US with annual sales over $50 billion from 69,900 total farms. California is also the sole producer in the US of 17 crops including figs, artichokes and almonds. Additionally, California leads organic sales, accounting for 40% of all organic crop production and 18.16% of United States Department of Agriculture certified organic farms. Many organic farms are small-scale and diversified and these type of DSSF sell food directly to consumers through marketing channels, such as farmers markets or Community Supported Agriculture programs. To suit the unique characteristics of California’s diverse, and within interior valley regions, year-round growing environment, we adjusted the USDA-ERS definition of “small-scale farm” to encompass operations that gross less than $500,000 annually and market directly to consumers through farmers markets, farm stands, CSAs, etc. DSSF are defined as those operations that grow a combination of livestock and specialty crops or raise multiple livestock species with the intent of selling sustainably-raised animal products directly to consumers. Some diversified farms integrate livestock and crop production by using their animals to graze crop residues or cover crops before planting with fresh market crops. Grazing enhances soil fertility, recycles farm nutrients and animals provide another source of revenue through fiber or food products.

Many consumers perceive small-scale farms or outdoor-raised livestock as more natural and safer than food grown on large-scale conventional farms or meat animals raised in confinement systems, but animals naturally harbor food borne pathogens that can cause severe human illness, like Salmonella spp., Campylobacter spp. and Shiga toxin-producing Escherichia coli . For instance, a study by Patterson et al calculated a 4.17% prevalence of STEC in sheep raised on a diversified organic farm in California. Animals are intermittent shedders of enteric pathogens and shedding may increase under certain conditions, such as during periods of stress or due to husbandry practices . Many food borne pathogens can exist in the soil for extended periods of time and can be transmitted to humans through direct contact with feces or animals, or indirect contact with a contaminated environment or through ingestion of produce, meat or water. STEC is consistently one of the major pathogens involved in food borne outbreaks in the US. Vegetables and fruit consumed raw, including spinach, tomatoes and melons, are especially considered high-risk foods. In the summer of 2011, a small family farm u-pick berry operation was the center of an E. coli O157:H7 outbreak when strawberries were contaminated by wild deer feces. Six of the fifteen cases were hospitalized and two people died. More recently, several nationwide outbreaks of E. coli O157:H7 have occurred through consumption of romaine lettuce, including one outbreak traced back to California farms and linked to cattle grazing upstream from the lettuce fields. STEC outbreaks associated with DSSF might be under reported, due to their smaller volume of sales compared to large farms. A study by Harvey et al identified six STEC outbreaks connected with organic agricultural operations between 1992-2014. All these food borne outbreaks underscore the need to conduct prevalence studies of food borne pathogens on DSSF. Swine are especially a livestock species of concern because they are reservoirs for zoonotic diseases like swine influenza and brucellosis and food borne pathogens like STEC and Campylobacter spp. Although most swine production in the US occurs inside buildings with high levels of bio-security, draining pots the US is currently experiencing a resurgence of outdoor-based swine operations, due to consumer demand for sustainably-raised animal products. Still primarily considered a niche production system in the US, outdoor-raised pig operations  are numerous and broadly distributed within California. The USDA National Animal Health Monitoring System swine report defined “small-enterprise operations” as those raising fewer than 100 pigs. Approximately 68.8 – 78.9% of the small operations included in this nationwide survey raised domestic pigs with some level of outside access. A challenge in raising domestic pigs outdoors is the increasing risk of their directly or indirectly interacting with wildlife like feral pigs, and a subsequent potential increase for pathogen sharing, especially as feral pig abundance and distribution grows throughout the US. Feral pigs are considered an invasive species as they only need water, food and shrub cover to survive, can double their population in four months and are difficult to eradicate., Moreover, if an area contains favorable habitat for feral pigs, then their population numbers can be maintained or increase over time. They also have the widest geographic distribution and one of the broadest habitat ranges of any large mammal except humans.

The wide distribution of feral swine is in part due to their ability to adapt to many ecological habitats and their opportunistic omnivore diet. California has one of the largest and widest distributions of feral pigs. Feral pigs in the US are a mix of introduced Eurasian wild boars, which are native to Asia and Europe, and domestically-raised pigs turned feral. As early as 2005, Corn et. al described the disease implications of expanding feral pig populations in the US, because they can serve as a vehicle for pathogen transmission to domestic pigs, and they could play a significant role in the transmission and maintenance of transboundary animal diseases , that may be introduced or re-introduced to North America , classical swine fever). Other studies have also reported the disease risks from the expanding distribution of feral pigs in the US, including their future role as spreaders of TBD like ASF, which was recently found in the Dominican Republic, a mere 700 miles from Florida, US. Additionally, eradicated diseases in indoor-pig herds have been documented in feral swine populations in California, for example, feral pig samples collected by the California Department of Fish and Wildlife from 1978- 2013 showed feral pigs testing positive for Brucella suis, Leptospira spp. and swine influenza virus . Contact between feral pigs and outdoor-raised pig herds increases the risk for the transmission of these diseases in domestic swine. Many studies have reported that feral pigs maintain and transmit zoonotic and food borne pathogens; however, only a small subset of these studies focused on the risk of pathogen sharing between feral pigs and outdoor raised pigs. Transmission of pathogens between feral pigs and outdoor raised pigs has been documented in the US. For example, a 2016 human brucellosis case on a NewYork State farm began with a feral pig infecting domestic pigs reared outdoors. Swine sold from this index farm led to Brucella suis positive domestic swine in nine other herds in multiple states. Additionally, one swine brucellosis case each in Texas, Iowa and Georgia in 2005 also involved domestic swine being exposed to feral pigs through inadequate bio-security or wildlife controls. Feral pigs are known to forage on farmland and some California farmers and ranchers regularly experience feral pig intrusions in their crop fields and/or contact between outdoor raised pigs and feral pigs. According to studies conducted in California and Texas, contact has been documented between feral pigs and outdoor-raised pigs. A 2012 spatial study by Wyckoff et al reported that feral pigs are attracted to agricultural habitats as food sources, which may facilitate pathogen transmission to livestock raised outdoors and humans or contaminate crops. The authors assessed habitat and movement of feral swine within 10 miles of outdoor domestic pig operations in Texas and calculated that at least 50% of these facilities were surrounded by suitable feral pig habitat. Another Wyckoff et al study assessed the disease transmission risk of feral pigs near domestic pigs facilities in Texas. This 2009 study used GPS collars to quantify contact between feral and domestic pigs and detected evidence of direct contact, as well as antibodies for the same diseases in both swine groups. They concluded that feral swine are an increasing risk for the reintroduction of eradicated diseases as well as emerging TBD, especially for operations that allowed domestic swine outdoor access, as male feral pigs are attracted to female pens. International studies have also assessed the risk of disease transmission at the wild boar-domestic pig interface.