scholarly journals Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

2017 ◽  
Author(s):  
Kirill Grigorev ◽  
Sergey Kliver ◽  
Pavel Dobrynin ◽  
Aleksey Komissarov ◽  
Walter Wolfsberger ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Selection Signatures ◽  
Caribbean Islands ◽  
Assembly Strategy ◽  
Genome Data ◽  
String Graph ◽  
Additional Sequence ◽  
The Caribbean ◽  
Genome Assemblies

AbstractSolenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species’ genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

scholarly journals Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

2021 ◽  
Author(s):  
Wayne Xu ◽  
James R Tucker ◽  
Wubishet A Bekele ◽  
Frank M You ◽  
Yong-Bi Fu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
Barley Cultivar ◽  
Malting Barley ◽  
Orthologous Genes ◽  
Hordeum Vulgare L ◽  
Chromosome Conformation ◽  
Mate Pair ◽  
Genome Assemblies ◽  
First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

scholarly journals Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1972 ◽  
Author(s):  
Amy L. Longmuir ◽  
Peter L. Beech ◽  
Mark F. Richardson
Keyword(s):  
Plant Pathogen ◽  
Reference Genome ◽  
Phytophthora Cinnamomi ◽  
Gene Prediction ◽  
Single Copy ◽  
Draft Assembly ◽  
Protein Encoding ◽  
Pathogen Control ◽  
Genome Assemblies ◽  
Encoding Genes

Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings:  Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

Geology and hydrogeology of the Caribbean islands aquifer system of the Commonwealth of Puerto Rico and the U.S. Virgin Islands

2002 ◽  
Author(s):  
Robert A. Renken ◽  
W. C. Ward ◽  
I.P. Gill ◽  
Fernando Gómez-Gómez ◽  
Jesús Rodríguez-Martínez ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Virgin Islands ◽  
Aquifer System ◽  
Caribbean Islands ◽  
The Caribbean ◽  
The U.S

Leishmania spp. and leishmaniasis on the Caribbean islands

2019 ◽  
Author(s):  
Chaoqun Yao
Keyword(s):  
Puerto Rico ◽  
Dominican Republic ◽  
Trinidad And Tobago ◽  
Parasite Species ◽  
Sand Fly ◽  
Caribbean Islands ◽  
Leishmania Spp ◽  
The Caribbean ◽  
Human Infections ◽  
Sand Fly Vectors

Abstract The kinetoplastid protozoan Leishmania spp. cause leishmaniasis, which clinically exhibit mainly as a cutaneous, mucocutanous or visceral form depending upon the parasite species in humans. The disease is widespread geographically, leading to 20 000 annual deaths. Here, leishmaniases in both humans and animals, reservoirs and sand fly vectors on the Caribbean islands are reviewed. Autochthonous human infections by Leishmania spp. were found in the Dominican Republic, Guadeloupe and Martinique as well as Trinidad and Tobago; canine infections were found in St. Kitts and Grenada; and equine infections were found in Puerto Rico. Imported human cases have been reported in Cuba. The parasites included Leishmania amazonensis, Le. martiniquensis and Le. waltoni. Possible sand fly vectors included Lutzomyia christophei, Lu. atroclavatus, Lu. cayennensis and Lu. flaviscutellata as well as Phlebotomus guadeloupensis. Reservoirs included rats, rice rats and mouse opossum. An updated study is warranted for the control and elimination of leishmaniasis in the region because some of the data are four decades old.

scholarly journals Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

2021 ◽  
Vol 9 (3) ◽  
pp. 465
Author(s):  
Anne A. M. J. Becker ◽  
KC Hill ◽  
Patrick Butaye
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Taxonomic Diversity ◽  
Caribbean Islands ◽  
Microbial Profile ◽  
Vegetation Zones ◽  
Males And Females ◽  
The Caribbean ◽  
Metabolic Properties ◽  
Small Indian Mongoose

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

scholarly journals Chikungunya Fever in Japan Imported from the Caribbean Islands

2016 ◽  
Vol 69 (2) ◽  
pp. 151-153 ◽  
Author(s):  
Kazuo Imai ◽  
Eri Nakayama ◽  
Takuya Maeda ◽  
Kei Mikita ◽  
Yukiko Kobayashi ◽  
...  
Keyword(s):  
Chikungunya Fever ◽  
Caribbean Islands ◽  
The Caribbean

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

scholarly journals Maternal Infection and Adverse Pregnancy Outcomes among Pregnant Travellers: Results of the International Zika Virus in Pregnancy Registry

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 341
Author(s):  
Manon Vouga ◽  
Léo Pomar ◽  
Antoni Soriano-Arandes ◽  
Carlota Rodó ◽  
Anna Goncé ◽  
...  
Keyword(s):  
Pregnancy Outcomes ◽  
Adverse Pregnancy Outcomes ◽  
Minimal Risk ◽  
Maternal Infection ◽  
Caribbean Islands ◽  
Multicentre Cohort Study ◽  
Epidemic Period ◽  
The Caribbean ◽  
Adverse Pregnancy ◽  
Multicentre Cohort

In this multicentre cohort study, we evaluated the risks of maternal ZIKV infections and adverse pregnancy outcomes among exposed travellers compared to women living in areas with ZIKV circulation (residents). The risk of maternal infection was lower among travellers compared to residents: 25.0% (n = 36/144) versus 42.9% (n = 309/721); aRR 0.6; 95% CI 0.5–0.8. Risk factors associated with maternal infection among travellers were travelling during the epidemic period (i.e., June 2015 to December 2016) (aOR 29.4; 95% CI 3.7–228.1), travelling to the Caribbean Islands (aOR 3.2; 95% CI 1.2–8.7) and stay duration >2 weeks (aOR 8.7; 95% CI 1.1–71.5). Adverse pregnancy outcomes were observed in 8.3% (n = 3/36) of infected travellers and 12.7% (n = 39/309) of infected residents. Overall, the risk of maternal infections is lower among travellers compared to residents and related to the presence of ongoing outbreaks and stay duration, with stays <2 weeks associated with minimal risk in the absence of ongoing outbreaks.

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