Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Background

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species’ exceptionally long life span.

Findings

We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing–assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored.

Conclusions

We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.

Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness

Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies has neglected the impact of ecological interactions. Dynamics among microbial communities, host immune responses, and environmental conditions may alter the effect of probiotics in human and veterinary medicine, agriculture and aquaculture, and the proposed treatment of emerging wildlife and zoonotic diseases such as those occurring on amphibians or vectored by mosquitoes. Here we use a holistic measure of amphibian mucosal defenses to test the effects of probiotic treatments and to assess disease risk under different ecological contexts. We developed a non-invasive assay for antifungal function of the skin mucosal ecosystem (mucosome function) integrating host immune factors and the microbial community as an alternative to pathogen exposure experiments. From approximately 8500 amphibians sampled across Europe, we compared field infection prevalence with mucosome function against the emerging fungal pathogen Batrachochytrium dendrobatidis. Four species were tested with laboratory exposure experiments, and a highly susceptible species, Alytes obstetricans, was treated with a variety of temperature and microbial conditions to test the effects of probiotic therapies and environmental conditions on mucosome function. We found that antifungal function of the amphibian skin mucosome predicts the prevalence of infection with the fungal pathogen in natural populations, and is linked to survival in laboratory exposure experiments. When altered by probiotic therapy, the mucosome increased antifungal capacity, while previous exposure to the pathogen was suppressive. In culture, antifungal properties of probiotics depended strongly on immunological and environmental context including temperature, competition, and pathogen presence. Functional changes in microbiota with shifts in temperature provide an alternative mechanistic explanation for patterns of disease susceptibility related to climate beyond direct impact on host or pathogen. This nonlethal management tool can be used to optimize and quickly assess the relative benefits of probiotic therapies under different climatic, microbial, or host conditions.

Stability of microbiota facilitated by host immune regulation: informing probiotic strategies to manage amphibian disease

Microbial communities can augment host immune responses and probiotic therapies are under development to prevent or treat diseases of humans, crops, livestock, and wildlife including an emerging fungal disease of amphibians, chytridiomycosis. However, little is known about the stability of host-associated microbiota, or how the microbiota is structured by innate immune factors including antimicrobial peptides (AMPs) abundant in the skin secretions of many amphibians. Thus, conservation medicine including therapies targeting the skin will benefit from investigations of amphibian microbial ecology that provide a model for vertebrate host-symbiont interactions on mucosal surfaces. Here, we tested whether the cutaneous microbiota of Panamanian rocket frogs, Colostethus panamansis, was resistant to colonization or altered by treatment. Under semi-natural outdoor mesocosm conditions in Panama, we exposed frogs to one of three treatments including: (1) probiotic - the potentially beneficial bacterium Lysinibacillus fusiformis, (2) transplant – skin washes from the chytridiomycosis-resistant glass frog Espadarana prosoblepon, and (3) control – sterile water. Microbial assemblages were analyzed by a culture-independent T-RFLP analysis. We found that skin microbiota of C. panamansis was resistant to colonization and did not differ among treatments, but shifted through time in the mesocosms. We describe regulation of host AMPs that may function to maintain microbial community stability. Colonization resistance was metabolically costly and microbe-treated frogs lost 7–12% of body mass. The discovery of strong colonization resistance of skin microbiota suggests a well-regulated, rather than dynamic, host-symbiont relationship, and suggests that probiotic therapies aiming to enhance host immunity may require an approach that circumvents host mechanisms maintaining equilibrium in microbial communities.

Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

Background

Rescuing amphibian diversity is an achievable conservation challenge. Disease mitigation is one essential component of population management. Here we assess existing disease mitigation strategies, some in early experimental stages, which focus on the globally emerging chytrid fungus Batrachochytrium dendrobatidis. We discuss the precedent for each strategy in systems ranging from agriculture to human medicine, and the outlook for each strategy in terms of research needs and long-term potential.

Results

We find that the effects of exposure to Batrachochytrium dendrobatidis occur on a spectrum from transient commensal to lethal pathogen. Management priorities are divided between (1) halting pathogen spread and developing survival assurance colonies, and (2) prophylactic or remedial disease treatment. Epidemiological models of chytridiomycosis suggest that mitigation strategies can control disease without eliminating the pathogen. Ecological ethics guide wildlife disease research, but several ethical questions remain for managing disease in the field.

Conclusions

Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.

Oral toxicity of boric acid and other boron compounds to immature cat fleas (Siphonaptera: Pulicidae)

Oral toxicity was characterized in first-instar cat fleas, Ctenocephalides felis felis (Bouché), feeding on dried blood treated with boric acid. LC50 values ranged from 2.11% after 24 h to 0.21% after 7 d. In carpet tests with five different boron compounds and a number of different formulations, significant mortality for first instars was observed in all cases. In similar tests with prepupae and cocoons, there was no significant effect on mortality. The importance of these results is discussed in light of current application procedures for boron compounds, and suggestions are made for future research.

Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins

The silent mating-type loci of Saccharomyces cerevisiae, HML and HMR, are flanked by transcriptional silencers that have ARS activity (i.e., they function as replication origins when in plasmids). To test whether these ARS elements are chromosomal origins, we mapped origins near HML (close to the left telomere of chromosome III). Our results indicate that the HML-associated ARS elements either do not function as chromosomal replication origins or do so at a frequency below our detection level, suggesting that replication from a silencer-associated origin in each S phase is not essential for the maintenance of transcriptional repression at HML. Our results also imply that the ability of a DNA fragment to function as an ARS element in a plasmid does not ensure its ability to function as an efficient chromosomal replication origin. Telomere proximity is not responsible for inactivating these ARS elements, because they are not detectably functional as chromosomal origins even in genetically modified strains in which they are far from the telomere.

Close association of a DNA replication origin and an ARS element on chromosome III of the yeast, Saccharomyces cerevisiae

Two dimensional gel electrophoretic techniques were used to locate all functional DNA replication origins in a 22.5 kb stretch of yeast chromosome III. Only one origin was detected, and that origin is located within several hundred bp of an ARS element.

The in vivo replication origin of the yeast 2 microns plasmid

We have used two-dimensional neutral/alkaline agarose gel electrophoresis to separate the nascent strands of replicating yeast 2 micron plasmid DNA molecules according to extent of replication, away from nonreplicating molecules and parental strands. Analysis of the lengths of nascent strands by sequential hybridization with short probes shows that replication proceeds bidirectionally from a single origin at map position 3700 +/- 100, coincident with the genetically mapped ARS element. The two recombinational isomers of 2 microns plasmid (forms A and B) replicate with equal efficiency. These results suggest that ARS elements may prove to be replication origins for chromosomal DNA.

Neonatal screening for sickle cell diseases in Camberwell: results and recommendations of a two year pilot study

The sickle cell diseases are a major health problem for Afro-Caribbean peoples. Neonatal detection and prophylactic management can reduce mortality and morbidity in childhood. A study was therefore conducted analysing the results of the first two years of cord blood screening in the Camberwell health area. Thirteen cases of sickle cell disease and two of haemoglobin (Hb)C disease were identified among 2202 non-white infants screened. The carrier state, sickle cell trait (HbAS), was present in 11.9% and HbC trait (HbAC) in 4.1% of Afro-Caribbean infants. The incidence of disease and of carrier states was much higher in West Africans than in Caribbeans. The wider implications of screening and the need for a comprehensive plan of care are emphasised.

Normal blood cell values in the early mid-trimester fetus

Samples of pure fetal blood from 116 fetuses of 15-21 weeks' gestation were obtained by direct vision fetoscopy. Ninety nine of these fetuses, presumed to be haematologically normal, were suitable for analysis. The data obtained show that the erythropoietic system is evolving rapidly in this gestational age range. The myeloid series shows no significant increase or decrease in numbers apart from eosinophils and basophils which increase significantly with gestational age whereas the platelet count remains constant. The growing application of fetoscopic blood sampling to the prenatal diagnosis and management of fetal blood disorders renders mandatory a knowledge of normal fetal blood values.

Experimental parvoviral infection in humans

Healthy adult volunteers were inoculated intranasally with human parvovirus obtained from an asymptomatic blood donor. One week after inoculation, intense viremia was observed in seronegative volunteers, accompanied by a mild illness with pyrexia, malaise, myalgia, itching, and excretion of virus from the respiratory tract. In the following week hematologic studies revealed reticulocytopenia with an associated slight drop in hemoglobin concentration, lymphopenia, neutropenia, and a drop in platelet counts. At 17-18 days after inoculation a second-phase illness with rash and arthralgia lasting three to four days occurred in three of four infected volunteers. This study confirms the etiologic role of human parvovirus in erythematous rash illness, with the second-phase illness being consistent with adult cases of erythema infectiosum. Moreover, the hematologic changes associated with infection support the hypothesis that the same virus is responsible for the temporary arrest of erythropoiesis that leads to aplastic crisis in persons with chronic hemolytic anemia.

Occurrence of infection with a parvovirus-like agent in children with sickle cell anaemia during a two-year period

The occurrence of infection with a parvovirus-like agent during the period April 1979-May 1981 in children attending a single sickle cell clinic in London was investigated. Virus was detected in serum by counter-current immunoelectrophoresis (CIE) and immunoelectron microscopy (IEM). Viral antibody was detected by CIE and specific IgM antibody by an IgM-antibody capture assay. Of the 68 children studied nine presented in aplastic crisis and evidence of infection with the parvovirus-like agent at the time of the crisis was found in all nine. Eighteen of the other children were antibody-positive at some time during the study. In 11 children there was no evidence of recent infection; however, two of these had a history of aplastic crisis in previous years. The other seven seroconverted during the course of the study but did not show any haematological effects. Five of these had a primary infection, one appeared to have reinfection and in the seventh there were insufficient data to distinguish between the two. Possible explanations for the difference between those presenting with aplastic crisis and those with asymptomatic seroconversion are discussed.

Both parental deoxyribonucleic acid strands at each replication fork of replicating simian virus 40 chromosomes are cut by a single-strand-specific endonuclease

We have measured the relative accessibility to a single-strand-specific endonuclease of the single-stranded DNA on the leading and lagging sides of replication forks in replicating simian virus 40 (SV40) chromosomes. To do this we have digested replicating SV40 chromosomes with a single-strand-specific endonuclease (P1 nuclease) and then characterized the intermediate and final products of digestion by sucrose gradient sedimentation and agarose gel electrophoresis. P1 nuclease rapidly and specifically cleaves parental DNA strands at replication forks, yielding intermediate and final cleavage products which are consistent with an approximately equal rate of nuclease cleavage on both sides of the fork. Thus, single-stranded DNA is approximately as accessible to P1 nuclease on the leading side of the fork as on the lagging side; the simplest interpretation of this observation is that the stretch of single-stranded DNA on the leading side is as long as that on the lagging side.

Defective yeast opsonisation and functional deficiency of complement in sickle cell disease

Opsonisation of heat-killed baker's yeast, functional activity of the total alternative pathway of complement, and factor B detected functionally and immunochemically were significantly reduced in 72 children with sickle cell disease compared with 40 age-matched black control children. There was significant correlation between functional activity of the total alternative pathway and functionally measured factor B, but not between factor B measured functionally and immunochemically. The opsonisation defect could be corrected in vitro by normal serum, and factor B-depleted serum, and was qualitatively similar to that seen in patients with primary yeast opsonisation deficiency. Serial studies showed that these serum defects were persistent. Reduction in the activity of components of the alternative pathway of complement and opsonisation was found in 4 patients who had recovered from pneumococcal meningitis and in one who developed osteomyelitis. Defects of yeast opsonisation and complement which are common in patients with sickle cell disease, may partly explain the children's increased susceptibility to infection, and might help to identify individuals especially at risk.

The development and use of an antibody capture radioimmunoassay for specific IgM to a human parvovirus-like agent

An IgM-antibody capture radioimmunoassay (MACRIA) was developed for the detection of IgM antibody specific for the human parvovirus-like agent B19. Diagnosis of infection with this agent by either antigen detection or antibody seroconversion had been made by counter-current immunoelectrophoresis (CIE) in 18 cases of aplastic crisis occurring in children with homozygous sickle-cell disease. The MACRIA described here gave positive results in 17 of these 18 cases; in the remaining case only an acute specimen taken from the patient during viraemia and late convalescent specimens taken 184 and 247 days after onset of illness were available. The test was used to investigate 20 further cases of aplastic crisis in which neither viral antigen nor antibody seroconversion could be detected by CIE. Detection of virus-specific IgM permitted diagnosis of infection with this parvovirus-like agent in 17 of these cases. In the remaining three cases only single serum specimens taken late in convalescence, 82 days or more after the onset of symptoms, were available. In addition to these 34 cases of aplastic crisis in which primary infection with this agent was diagnosed by MACRIA, seven cases of apparent 'silent' infection detected by CIE were investigated. The test permitted the discrimination between primary infection and re-exposure to the virus in six of these patients. The use of this assay has added a considerable weight of evidence implicating primary infection with this parvovirus-like agent as an important cause of aplastic crisis in children with sickle-cell disease. Furthermore, MACRIA permits diagnosis of infection when only single serum specimens taken up to ten weeks after infection are available. Thus the use of this test will significantly facilitate the investigation of other clinical syndromes of presumptive infectious aetiology.

Survey of sickle-cell disease in England and Wales

The incidence and the clinical course of patients suffering from sickle-cell syndrome (Hb SS; Hb SC; Hb S thal) in England and Wales are not known. In 1979 an ad hoc committee was formed to investigate these problems. Initially, a questionnaire was sent to 227 haematologists in England and Wales to determine the number of cases in these countries. The replies have indicated that 1367 cases were seen in 1978 and 1979. Probably this may represent only half the total number of cases. From this survey it has been possible to draw up a composite map showing the location of patients, which has provided a basis to determine the clinical course of the disease, and for further studies into the complications and management of sickle-cell disease in England and Wales. From a second questionnaire preliminary data about the general management and mortality in England and Wales have been recorded.

Admissions to hospital of children with sickle-cell anaemia: a study in south London

Admissions to hospital of 171 children with sickle-cell anaemia, genotype Hb SS, were reviewed over a 20-year period. Altogether 887 admissions occurred in 797 patient-years. The commonest cause of admission was painful vaso-occlusive crisis. Appreciable morbidity also resulted from pulmonary disease, infection, and anaemic episodes. The complications resulting in the most severe illness were acute splenic sequestration, pneumococcal meningitis, and some episodes of erythroid hypoplasia resulting in very low haemoglobin concentrations. Most deaths occurred in children aged under 5. Mortality and morbidity could be reduced by measures including prophylaxis of pneumococcal infections and more active treatment of seemingly minor illness in children with sickle-cell anaemia.

Copper chelate affinity chromatography of human fibroblast and leucocyte interferons

Human fibroblast and human leucocyte interferons display a strong affinity for the copper chelate of bis-carboxymethyl amino agarose, binding tenaciously over a wide pH range (7.4 to 4.0). Their binding is apparently irreversible on a sorbent saturated with copper (24.8 mumol of Cu2+/ml of column bed). However, both interferons can be partially recovered from sorbents of lower copper content, prepared by leaching the columns with sodium citrate at pH 9.0. The recovery of fibroblast interferon from a leached sorbent (5.8 mumol of Cu2+/ml of column bed) is about 30% and that of leucocyte interferon about 60%. Moreover, the strength of binding of leucocyte interferon can be modulated by leaching copper chelate-agarose with citrate of varying concentration.

Value of serum ferritin estimation in sickle cell anaemia

In a group of 35 children with sickle cell anaemia serum ferritin concentration ranged from 70 to 2460 microgram/l (mean 367, median 180 microgram/l). This was significantly higher than the ferritin levels (range 8-101, mean 34, median 30 microgram/l) in a group of 63 normal control children of the same age group. 30 (86%) of the sickle cell children showed serum ferritin levels greater than 101 microgram/l, and 2 (6%) levels greater than 1000 microgram/l. 7 of the patients had not been transfused before this study. Their serum ferritin levels were all raised and showed a significant correlation with age but not with haemoglobin level. In the remainder of the patients the serum ferritin bore no significant correlation with age, haemoglobin level, or number of units of blood transfused. 2 children with HbSC disease had levels within the control range. Since patients with sickle cell anaemia have an increasing chance of long survival, we suggest that serial estimations of their iron status be made by means of serum ferritin assay in order to determine which patients are accumulating excessive iron.

Serum-alpha-hydroxybutyrate dehydrogenase levels in sickle-cell disease and sickle-cell crisis

In patients with sickle-cell disease (Hb S/S disease) who are not in crisis, the serum-level of alpha-hydroxybutyrate dehydrogenase (alpha-H.B.D.) is significantly above normal. The degree of elevation correlates with the severity of the disease. During infarctive crises the level increases still further by a factor of 2 to 3, and it returns to the patient's normal level on recovery. The level of alpha-H.B.D. thus provides an index of the severity of the disease. Also, it allows distinction between true infarctive crisis, infection, and fake symptoms. In 5 patients a rise in the level of alpha-H.B.D. above the patient's normal level was detected several days before the onset of symptoms, which suggests that there may be a "prodromal" phase.

Changing blood picture in sickle-cell anaemia from shortly after birth to adolescence

The blood picture of children with sickle-cell anaemia was found to change with age. The changes were most marked in the first year but the mean level of haemoglobin, haemoglobin F, and target cells fell until adolescence, and irreversibly sickled cells rose. Reticulocytes, Howell Jolly bodies, and normablasts altered little after one year. The fall in haemoglobin F suggested a delayed changeover from fetal to adult haemoglobin production. It was concluded that the blood changes in sickle-cell anaemia were progressive throughout childhood.

Failure of laboratory and radiological studies to predict jejunal mucosal atrophy

Of 58 children with suspected malabsorption, 27 were shown to have subtotal or partial atrophy, and 31 had normal mucosal histology. Oral glucose tolerance tests, faecal fat excretion, D-xylose excretion tests, Prosparol absorption studies, haematological investigations, and radiological examination of the small bowel failed to distinguish these two groups and frequently gave misleading results. It is concluded that in suspected coeliac disease small intestinal biopsy should be performed as a primary investigation.

Target cells in haemoglobinopathies

A semi-quantitative method of estimating the number of target cells in blood films has been developed. It has been applied to 250 films from normal persons, pregnant women, and patients with a variety of haemoglobinopathies. Allowing for the frequency of target cells found in normal films the results show that such an examination is of value in eliminating or suggesting certain haemoglobinopathies, but not in excluding the majority of the traits.