Genomic consequences of isolation and inbreeding in an island dingo population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Genomic consequences of isolation and inbreeding in an island dingo population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Genomic signatures of bottleneck and founder effects in dingoes.

Dingoes arrived in Australia during the mid-Holocene and are the top-order terrestrial predator on the continent. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. We investigated this hypothesis by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6-4.7 times higher than in other canines. While examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous-to-synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes in mainland Australia. These findings highlight the need for conservation-based management of dingoes and the need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.

Genomic footprints of bottleneck in landlocked salmon population.

At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and ponds of the Northern Hemisphere. Occasionally, the populations also got locked when the flow of rivers terminated from reaching the sea due to land upheaval. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers. According to the theories of population genetics, the effect of genetic drift is expected to be more pronounced in the former compared to the latter. Here we examined this using the whole genome data of landlocked and anadromous salmon populations of Norway. Our results showed a 50-80% reduction in the genomic heterozygosity in the landlocked compared to anadromous salmon populations. The number and total size of the runs of homozygosity (RoH) segments of landlocked salmons were two to eightfold higher than those of their anadromous counterparts. We found the former had a higher ratio of nonsynonymous-to-synonymous diversities than the latter. The investigation also revealed a significant elevation of homozygous deleterious Single Nucleotide Variants (SNVs) in the landlocked salmon compared to the anadromous populations. All these results point to a significant reduction in the population size of the landlocked salmons. This process of reduction might have started recently as the phylogeny revealed a recent separation of the landlocked from the anadromous population. Previous studies on terrestrial vertebrates observed similar signatures of a bottleneck when the populations from Island and the mainland were compared. Since landlocked waterbody such as ponds and lakes are geographically analogous to Islands for fish populations, the findings of this study suggest the similarity in the patterns of evolution between the two.

The Difference in the Proportions of Deleterious Variations within and between Populations Influences the Estimation of FST.

Estimating the extent of genetic differentiation between populations is an important measure in population genetics, ecology and evolutionary biology. The fixation index, or FST, is an important measure, which is routinely used to quantify this. Previous studies have shown that the FST estimated for selectively constrained regions was significantly lower than that estimated for neutral regions. By deriving the theoretical relationship between FST at neutral and constrained sites, we show that excess in the fraction of deleterious variations segregating within populations compared to those segregating between populations is the cause for the reduction in FST estimated at constrained sites. Using whole-genome data, our results revealed that the magnitude of reduction in FST estimates obtained for selectively constrained regions was much higher for distantly related populations compared to those estimated for closely related pairs. For example, the reduction was 47% for comparison between Europeans and Africans, 30% for the European and Asian comparison, 16% for the Northern and Southern European pair, and only 4% for the comparison involving two Southern European (Italian and Spanish) populations. Since deleterious variants are purged over time due to purifying selection, their contribution to the among-population diversity at constrained sites decreases with the increase in the divergence between populations. However, within-population diversities remain the same for all pairs compared; therefore, the FST estimated at constrained sites for distantly related populations are much smaller than those estimated for closely related populations. We obtained similar results when only the SNPs with similar allele frequencies at neutral and constrained sites were used. Our results suggest that the level of population divergence should be considered when comparing constrained site FST estimates from different pairs of populations.

NMOSD and MS prevalence in the Indigenous populations of Australia and New Zealand.

BACKGROUND: We studied the prevalence of neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) in Indigenous populations of Australia and New Zealand with the aim of assessing potential differences. METHODS: Cases of possible NMOSD and MS were collected from Australia and New Zealand. Clinical details, MR imaging, and serologic results were used to apply 2015 IPND diagnostic criteria for NMOSD and 2010 McDonald criteria for MS. Frequencies of self-determined ethnic ancestry were calculated for confirmed NMOSD, suspected NMOSD, and MS. Prevalence rates for NMOSD and MS according to ancestry were compared. RESULTS: There were 75 cases with NMOSD, 89 with suspected NMSOD, and 101 with MS. NMOSD cases were more likely to have Asian, Indigenous, or Other ancestry compared to suspected NMOSD or MS. There were no differences in the clinical phenotype of NMOSD seen in Indigenous compared to European ancestry populations. Per 100,000, the prevalence estimate for NMOSD in people with Maori ancestry was 1.50 (95% CI 0.52-2.49) which was similar to those with Asian ancestry 1.57 (95% CI 1.15-1.98). NMOSD prevalence in Australian Aboriginal and Torres Strait Islander populations was 0.38 (95% CI 0.00-0.80) per 100,000. CONCLUSION: The prevalence of NMOSD in the Maori population is similar to South East Asian countries, reflecting their historical origins. The prevalence of MS in this group is intermediate between those with South East Asian and European ancestry living in New Zealand. Both NMOSD and particularly MS appear to be uncommon in the Indigenous populations of Australia.

Deleterious protein-coding variants in diverse cattle breeds of the world.

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

Genomic Prediction for Whole Weight, Body Shape, Meat Yield, and Color Traits in the Portuguese Oyster Crassostrea angulata.

Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, Crassostrea angulata. The study consisted of 647 oysters: 188 oysters from 57 full-sib families from the first generation and 459 oysters from 33 full-sib families from the second generation. The number per family ranged from two to eight oysters for the first and 12-15 oysters for the second generation. After quality control, a set of 13,048 markers were analyzed to estimate the genetic parameters (heritability and genetic correlation) and predictive accuracy of the genomic selection for these traits. The multi-locus mixed model analysis indicated high estimates of heritability for meat yield traits: 0.43 for soft tissue weight and 0.77 for condition index. The estimated genomic heritabilities were 0.45 for whole weight, 0.24 for cup ratio, and 0.33 for fan ratio and ranged from 0.14 to 0.54 for color traits. The genetic correlations among whole weight, meat yield, and body shape traits were favorably positive, suggesting that the selection for whole weight would have beneficial effects on meat yield and body shape traits. Of paramount importance is the fact that the genomic prediction showed moderate to high accuracy for the traits studied (0.38-0.92). Therefore, there are good prospects to improve whole weight, meat yield, body shape, and color traits using genomic information. A multi-trait selection program using the genomic information can boost the genetic gain and minimize inbreeding in the long-term for this population.

Harmful mutation load in the mitochondrial genomes of cattle breeds.

OBJECTIVE: Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. RESULTS: Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

The Long-Term Evolutionary History of Gradual Reduction of CpG Dinucleotides in the SARS-CoV-2 Lineage.

Recent studies suggested that the fraction of CG dinucleotides (CpG) is severely reduced in the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The CpG deficiency was predicted to be the adaptive response of the virus to evade degradation of the viral RNA by the antiviral zinc finger protein that specifically binds to CpG nucleotides. By comparing all representative genomes belonging to the genus Betacoronavirus, this study examined the potential time of origin of CpG depletion. The results of this investigation revealed a highly significant correlation between the proportions of CpG nucleotide (CpG content) of the betacoronavirus species and their times of divergence from SARS-CoV-2. Species that are distantly related to SARS-CoV-2 had much higher CpG contents than that of SARS-CoV-2. Conversely, closely related species had low CpG contents that are similar to or slightly higher than that of SARS-CoV-2. These results suggest a systematic and continuous reduction in the CpG content in the SARS-CoV-2 lineage that might have started since the Sarbecovirus + Hibecovirus clade separated from Nobecovirus, which was estimated to be 1213 years ago. This depletion was not found to be mediated by the GC contents of the genomes. Our results also showed that the depletion of CpG occurred at neutral positions of the genome as well as those under selection. The latter is evident from the progressive reduction in the proportion of arginine amino acid (coded by CpG dinucleotides) in the SARS-CoV-2 lineage over time. The results of this study suggest that shedding CpG nucleotides from their genome is a continuing process in this viral lineage, potentially to escape from their host defense mechanisms.

Clinic-pathological aspect of gastro-intestinal stromal tumors at tertiary care Hospital India / Aspecto clínico e patológico dos tumores estromais gastrointestinais em hospital terciário da Índia

Abstract Background This study defines the disease profile in south Indian population and determine the clinic-pathological aspects of Gastro-Intestinal Stromal Tumors. Method In this prospective study patients diagnosed of gastrointestinal stromal tumors were taken thorough clinical examination and a database of Anthropometric details and clinical details were analyzed. Pathological data included tumor size, presence or absence necrosis, mitotic counts, immunohistochemistry for CD-117, CD-34. Results There were 44 patients with confirmed diagnosis of gastro-intestinal stromal tumor. The highest incidence was found in the 6th decade. The most common symptoms were abdominal pain and gastrointestinal bleed. Stomach was most frequent site for gastro-intestinal stromal tumors. Immunochemistry for CD-117 was positive in 93.18% cases. Majority of tumors (79.5%) had pure spindle cell morphology and mitotic activity showed that 34% of the GISTs were of the high risk group. Forty two patients were suggestive of surgery as the primary treatment after presentation. Conclusion Abdominal pain was the most common presenting complaint. Majority of the tumors aroused from the stomach. The majority of the tumors had pure spindle cell morphology and 93% of the tumors were CD-117 positive. A significant relationship between tumor size, tumor necrosis and mitotic activity with large tumors having necrosis and high mitotic rate having high risk of malignancy, was observed. Surgical resection is considered mainstay of treatment of gastro-intestinal stromal tumor. Imatinib therapy should be given to patients in moderate to severe risk categories.

Resumo Justificativa Este estudo define o perfil da doença na população do sul da Índia e determina os aspectos clínicos e patológicos dos tumores estromais gastrointestinais. Método Neste estudo prospectivo, os pacientes diagnosticados com tumor estromal gastrointestinl foram submetidos a um exame clínico completo, e uma série de dados dos pacientes, incluindo detalhes antropométricos e clínicos, foram analisados. Os dados patológicos incluíram tamanho do tumor, presença ou ausência de necrose, contagem mitótica e imuno-histoquímica para CD-117, CD-34. Resultados Havia 44 pacientes com diagnóstico confirmado de tumor estromal gastrointestinal. A maior incidência foi encontrada na 6ª década de vida. Os sintomas mais comuns foram dor abdominal e sangramento gastrointestinal. O estômago foi o local mais frequente para tumores estromais gastrointestinais. A imuno-histoquímica para CD-117 foi positiva em 93,18% dos casos. A maioria dos tumores (79,5%) apresentava morfologia pura de células fusiformes e a atividade mitótica mostrou que 34% dos GISTs pertenciam ao grupo de alto risco. Quarenta e dois pacientes receberam indicação para cirurgia como tratamento primário após a apresentação. Conclusão A dor abdominal foi a queixa mais comum. A maioria dos tumores afetava o estômago, apresentava morfologia pura de células fusiformes e 93% eram CD-117 positivos. Foi observada uma relação significativa entre o tamanho do tumor, a necrose tumoral e a atividade mitótica, com os tumores grandes apresentando necrose e alta taxa mitótica com alto risco de malignidade. A ressecção cirúrgica é considerada o principal tratamento do tumor estromal gastrointestinal. A terapia com imatinibe deve ser administrada a pacientes em categoria de risco de moderadas a grave.

A rectal gastrointestinal stromal tumor - a plea for neoadjuvant imatinib and TAMIS / Tumor estromal gastrointestinal no reto - um caso de uso de imatinibe neoadjuvante e TAMIS

Abstract Here we describe an infrequent case of gastrointestinal stromal tumor of the rectum in a 57 year-old man with spindle cell neoplasm probably gastrointestinal stromal tumor and CT scan showed tumor from the anterior rectal wall and offered abdominoperineal resection for the same. The patient was started on imatinib and had a significant reduction in symptoms. The patient was reassessed with the CT scan, which showed a reduction in tumor size and Transanal minimally invasive surgery was planned for the patient. Use of imatinib prior to surgical resection to attain the reduced size of the tumor within the limit of resection is an attractive approach. Since tumor development can happen rapidly again after substantial tumor shrinkage, the best time to operate depending on resectability and the maximum therapeutic outcome remains divisive.

Resumo No presente estudo, os autores descrevem um caso raro de tumor estromal gastrointestinal no reto em um homem de 57 anos que se apresentou com neoplasia de células fusiformes, com provável tumor estromal gastrointestinal. A tomografia computadorizada demonstrou tumor na parede anterior do reto e foi sugerida sua ressecção abdominoperineal. O paciente iniciou tratamento com imatinibe e apresentou uma redução significativa nos sintomas. O paciente foi reavaliado por tomografia computadorizada, que evidenciou redução do tamanho do tumor; portanto, foi indicada cirurgia transanal minimamente invasiva. O tumor era ressecável e foi necessário um extenso acompanhamento para romper o órgão, de forma a alcançar a ressecção máxima; caso contrário, o tumor estromal gastrointestinal também seria irressecável. O uso de imatinibe antes da ressecção cirúrgica para reduzir o tamanho do tumor dentro do limite de ressecção é uma abordagem interessante. Como o tumor pode se crescer rapidamente após ser substancialmente reduzido, a literatura ainda apresenta controvérsias quanto ao melhor momento para operar e quanto ao melhor desfecho terapêutico.

A study on the efficacy of single layer full thickness duct to mucosa pancreatojejunostomy following pancreatoduodenectomy.

OBJECTIVE: Pancreatoduodenectomy is the procedure of choice for treating periampullary and pancreatic head malignancy. The procedure has been standardized and the mortality has reduced considerably to fewer than 5% in high volume centers specializing in pancreatic surgeries. Unfortunately, the morbidity still hovers around 40%. The Achiles heal of pancreatoduodenectomy is the pancreatoenteric anastamosis, the failure of which leads to significant morbidity. Literature is flooded with a plethora of techniques of reconstruction, and the results are variable. In this present study, we have analyzed a technique in which we used a single layer full thickness duct to mucosa pancreatojejunostomy. Among the 25 subjects in this study, there was only one case of one mortality due to drug-induced cardiac arrhythmia, and no mortality secondary to pancreas-specific complications were reported. The present study was a pilot study compared with historical controls, where these results were comparable to the historical data reported earlier as well as our own historical data of two-layered anastamosis. The results of this pilot study supported our concept of single layer full thickness duct to mucosa anastamosis being least traumatic to the pancreas and having an equal efficacy to that other conventional techniques.

Population size influences the type of nucleotide variations in humans.

BACKGROUND: It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. RESULTS: Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (ß) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, ß showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high ß. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced ß. This was further confirmed by a positive relationship between Ne and ß for homozygous variants. CONCLUSIONS: Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs.

In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server. In the post-genomic era, researchers are able to obtain bioinformatically processed high-quality publication-ready whole genome data for many individuals in a population from next generation sequencing companies due to the reduction in the cost of sequencing and analysis. Such genotype data is typically presented in the Variant Call Format (VCF) and there is no simple software available that directly uses this data format to construct the phylogeny of populations in a short time. To address this limitation, we have developed a user-friendly software, VCF2PopTree that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes. For example, it reads a VCF file containing 4 million SNPs and draws a tree in less than 30 seconds. VCF2PopTree accepts genotype data from a local machine, constructs a tree using UPGMA and Neighbour-Joining algorithms and displays it on a web-browser. It also produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs. The software including the source code, a test VCF file and a documentation are available at: https://github.com/sansubs/vcf2pop.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

Greenlip Abalone (Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning.

Wild abalone (Family Haliotidae) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian 'greenlip' abalone (Haliotis laevigata, Donovan 1808) and generated 11 tissue transcriptomes from a female adult abalone. Phylogenetic analysis of the greenlip abalone with reference to the Pacific abalone (Haliotis discus hannai) indicates that these abalone species diverged approximately 71 million years ago. This study presents an in-depth analysis into the features of reproductive dysfunction, where we provide the putative biochemical messenger components (neuropeptides) that may regulate reproduction including gonad maturation and spawning. Indeed, we isolate the egg-laying hormone neuropeptide and under trial conditions induce spawning at 80% efficiency. Altogether, we provide a solid platform for further studies aimed at stimulating advances in abalone aquaculture production. The H. laevigata genome and resources are made available to the public on the abalone 'omics website, http://abalonedb.org.

Melioidosis-Series of Seven Cases from Madurai, Tamil Nadu, India.

We describe a case series of seven culture proven melioidosis patients presenting during 2014 to 2016 in Madurai, south Tamilnadu. Skin, soft tissue, bone and joint infections were common. All of them were middle aged men except one case. All the cases were reported during the monsoon season. Predisposing factors include diabetes and alcoholism. Despite many case reports and studies from South India, melioidosis still remains undiagnosed, hence under reported from many centers. Delayed diagnosis leads way to sepsis and other complications. Awareness about the preventive measures, earlier clinical and laboratory identification and appropriate management of severe sepsis are required to reduce the burden of this disease. HOW TO CITE THIS ARTICLE: Ganesan V, Sundaramoorthy R et al., Melioidosis-Series of Seven Cases from Madurai, Tamil Nadu, India. Indian J Crit Care Med 2019;23(3):149-151.

Ancient nuclear genomes enable repatriation of Indigenous human remains.

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves.

Oysters are keystone species in estuarine ecosystems and are of substantial economic value to fisheries and aquaculture worldwide. Contending with disease and environmental stress are considerable challenges to oyster culture. Here we report a draft genome of the Sydney Rock Oyster, Saccostrea glomerata, an iconic and commercially important species of edible oyster in Australia known for its enhanced resilience to harsh environmental conditions. This is the second reference genome to be reported from the family Ostreidae enabling a genus-level study of lophotrochozoan genome evolution. Our analysis of the 784-megabase S. glomerata genome shows extensive expansions of gene families associated with immunological non-self-recognition. Transcriptomic analysis revealed highly tissue-specific patterns of expression among these genes, suggesting a complex assortment of immune receptors provide this oyster with a unique capacity to recognize invading microbes. Several gene families involved in stress response are notably expanded in Saccostrea compared with other oysters, and likely key to this species' adaptations for improved survival higher in the intertidal zone. The Sydney Rock Oyster genome provides a valuable resource for future research in molluscan biology, evolution and environmental resilience. Its close relatedness to Crassostrea will further comparative studies, advancing the means for improved oyster agriculture and conservation.