scholarly journals Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

2019 ◽  
Author(s):  
Emily Humble ◽  
Pavel Dobrynin ◽  
Helen Senn ◽  
Justin Chuven ◽  
Alan F. Scott ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Captive Breeding ◽  
Demographic History ◽  
High Genetic Diversity ◽  
Contact Mapping ◽  
Sequencing Technologies ◽  
Captive Populations ◽  
Recent Developments ◽  
In The Wild ◽  
Negative Impacts

AbstractCaptive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

scholarly journals Somewhat saved: a captive breeding programme for two endemic Christmas Island lizard species, now extinct in the wild

Oryx ◽  
2016 ◽  
Vol 52 (1) ◽  
pp. 171-174 ◽  
Author(s):  
Paul Andrew ◽  
Hal Cogger ◽  
Don Driscoll ◽  
Samantha Flakus ◽  
Peter Harlow ◽  
...  
Keyword(s):  
Native Species ◽  
Captive Breeding ◽  
Biodiversity Loss ◽  
Breeding Programme ◽  
Lizard Species ◽  
Christmas Island ◽  
Captive Populations ◽  
Captive Breeding Programme ◽  
In Captivity ◽  
In The Wild

AbstractAs with many islands, Christmas Island in the Indian Ocean has suffered severe biodiversity loss. Its terrestrial lizard fauna comprised five native species, of which four were endemic. These were abundant until at least the late 1970s, but four species declined rapidly thereafter and were last reported in the wild between 2009 and 2013. In response to the decline, a captive breeding programme was established in August 2009. This attempt came too late for the Christmas Island forest skink Emoia nativitatis, whose last known individual died in captivity in 2014, and for the non-endemic coastal skink Emoia atrocostata. However, two captive populations are now established for Lister's gecko Lepidodactylus listeri and the blue-tailed skink Cryptoblepharus egeriae. The conservation future for these two species is challenging: reintroduction will not be possible until the main threats are identified and controlled.

scholarly journals Firefly Translocation: A Case Study of Genetic and Behavioral Evaluation in Thailand

2021 ◽  
Author(s):  
Anchana Thancharoen
Keyword(s):  
Success Rate ◽  
Captive Breeding ◽  
Large Population ◽  
Metropolitan Region ◽  
Success Rates ◽  
Captive Populations ◽  
In Captivity ◽  
In The Wild ◽  
Threatened Fauna

Conservation translocation is frequently used to conserve the threatened fauna by releasing individuals from the wild or captive populations into a particular area. This approach, however, is not successful in many cases because the translocated populations could not self-sustain in the new habitats. In this chapter, I reviewed the concept of translocation for conservation and the factors associated with the success rate. I used example problems from several cases involving different insect taxa. With its often high potential to mass rear in captivity, captive breeding can be a powerful tool by assuring large population size for insect translocation, which can result in a high success rate. However, genetic consequences from inbreeding and genetic adaptation to captivity can reduce the fitness of the captive population to establish successfully in the wild. Additionally, as the evidence in Japanese fireflies shows, the genetic differences between the translocated and local populations should be considered for a sustainable translocation program. A case study involved genetic and behavioral evaluation of S. aquatilis populations to assess the possibility of including the species for the firefly translocation program in Thailand. Although the results revealed no genetic variation among populations, examination of the variation in flash signals showed that the long-distance population had a longer courtship flash pulse than other populations in the Bangkok Metropolitan Region. With no geographical barrier, the light pollution and urbanization are probably important fragmented barriers causing adaptation of flash communication to increase the fitness. As a consequence, firefly translocation should consider flash variation between populations to prevent this potential pre-mating isolation mechanism from resulting in probable lower translocation success rates.

scholarly journals The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons)

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Rascha J. M. Nuijten ◽  
Mirte Bosse ◽  
Richard P. M. A. Crooijmans ◽  
Ole Madsen ◽  
Willem Schaftenaar ◽  
...  
Keyword(s):  
Endangered Species ◽  
Conservation Management ◽  
Demographic History ◽  
Genetic Research ◽  
Critically Endangered ◽  
Island Populations ◽  
Threatened And Endangered Species ◽  
Captive Populations ◽  
In Captivity ◽  
Recent Developments

The list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which often little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations ofS. cebifronsexist, which originated from two different Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to otherSusspecies potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well.

scholarly journals Getting off to a good start? Genetic evaluation of the ex situ conservation project of the Critically Endangered Montseny brook newt (Calotriton arnoldi)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3447 ◽  
Author(s):  
Emilio Valbuena-Ureña ◽  
Anna Soler-Membrives ◽  
Sebastian Steinfartz ◽  
Mònica Alonso ◽  
Francesc Carbonell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Genetic Material ◽  
Morphological Differentiation ◽  
Critically Endangered ◽  
Ex Situ ◽  
Wild Populations ◽  
Breeding Programs ◽  
Captive Populations ◽  
In The Wild

Ex situ management strategies play an important role in the conservation of threatened species when the wild survival of the species cannot be ensured. Molecular markers have become an outstanding tool for the evaluation and management of captive breeding programs. Two main genetic objectives should be prioritized when planning breeding programs: the maintenance of maximum neutral genetic diversity, and to obtain “self-sustaining” captive populations. In this study, we use 24 microsatellite loci to analyze and evaluate the genetic representativity of the initial phases of the captive breeding program of the Montseny brook newt, Calotriton arnoldi, an Iberian endemic listed as Critically Endangered. The results show that the initial captive stock has 74–78% of the alleles present in the wild populations, and captures roughly 93–95% of their total genetic diversity as observed in a previous study on wild newts, although it does not reach the desired 97.5%. Moreover, the percentage of unrelatedness among individuals does not exceed 95%. Therefore, we conclude that the genetic diversity of the captive stock should be improved by incorporating genetic material from unrelated wild newts. In recognition of the previously described significant genetic and morphological differentiation between eastern and western wild populations of C. arnoldi, we suggest maintaining two distinct breeding lines, and we do not recommend outbreeding between these lines. Our comparisons of genetic diversity estimates between real and distinct sample-sized simulated populations corroborated that a minimum of 20 individuals are needed for each captive population, in order to match the level of genetic diversity present in the wild populations. Thus, the current initial stock should be reinforced by adding wild specimens. The captive stock and subsequent cohorts should be monitored in order to preserve genetic variation. In order to avoid genetic adaptation to captivity, occasionally incorporating previously genotyped individuals from the wild into the captive populations is recommended.

scholarly journals Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid

2021 ◽  
Vol 12 ◽  
Author(s):  
Jhon Henry Trujillo-Montenegro ◽  
María Juliana Rodríguez Cubillos ◽  
Cristian Darío Loaiza ◽  
Manuel Quintero ◽  
Héctor Fabio Espitia-Navarro ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Saccharum Officinarum ◽  
Entire Genome ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Selection Processes ◽  
A Genome ◽  
Recent Developments ◽  
Sugarcane Hybrids

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.

scholarly journals Epigenomic regulation of heart failure: integrating histone marks, long noncoding RNAs, and chromatin architecture

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1713 ◽  
Author(s):  
Timothy A. McKinsey ◽  
Thomas M. Vondriska ◽  
Yibin Wang
Keyword(s):  
Heart Failure ◽  
Therapeutic Potential ◽  
Noncoding Rnas ◽  
Loss Of Function ◽  
Sequencing Technologies ◽  
Recent Developments ◽  
Non Coding Rnas ◽  
Epigenomic Regulation ◽  
Generation Sequencing ◽  
Epigenetic Processes

Epigenetic processes are known to have powerful roles in organ development across biology. It has recently been found that some of the chromatin modulatory machinery essential for proper development plays a previously unappreciated role in the pathogenesis of cardiac disease in adults. Investigations using genetic and pharmacologic gain- and loss-of-function approaches have interrogated the function of distinct epigenetic regulators, while the increased deployment of the suite of next-generation sequencing technologies have fundamentally altered our understanding of the genomic targets of these chromatin modifiers. Here, we review recent developments in basic and translational research that have provided tantalizing clues that may be used to unlock the therapeutic potential of the epigenome in heart failure. Additionally, we provide a hypothesis to explain how signal-induced crosstalk between histone tail modifications and long non-coding RNAs triggers chromatin architectural remodeling and culminates in cardiac hypertrophy and fibrosis.

scholarly journals Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

2019 ◽  
Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  
Keyword(s):  
Dark Matter ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Model Organism ◽  
Technology Choice ◽  
High Quality ◽  
Sequencing Technologies ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

scholarly journals The sources of sex differences in aging in annual fishes

2020 ◽  
Author(s):  
Martin Reichard ◽  
Radim Blažek ◽  
Jakub Žák ◽  
Petr Kačer ◽  
Oldřich Tomášek ◽  
...  
Keyword(s):  
Sex Differences ◽  
Social Environment ◽  
Social Factors ◽  
Environmental Conditions ◽  
Natural Populations ◽  
Experimental Results ◽  
Survival Difference ◽  
Captive Populations ◽  
Baseline Mortality ◽  
In The Wild

AbstractSex differences in lifespan and aging are widespread among animals, with males usually the shorter-lived sex. Despite extensive research interest, it is unclear how lifespan differences between the sexes are modulated by genetic, environmental and social factors. We combined comparative data from natural populations of annual killifishes with experimental results on replicated captive populations, showing that females consistently outlived males in the wild. This sex-specific survival difference persisted in social environment only in two most aggressive species, and ceased completely when social and physical contacts were prevented. Demographically, neither an earlier start nor faster rate of aging accounted for shorter male lifespans, but increased baseline mortality and the lack of mortality deceleration in the oldest age shortened male lifespan. The sexes did not differ in any measure of functional aging we recorded. Overall, we demonstrate that sex differences in lifespan and aging may be ameliorated by modulating social and environmental conditions.

scholarly journals The Many Faces of Astrocytes in Alzheimer's Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Michael D. Monterey ◽  
Haichao Wei ◽  
Xizi Wu ◽  
Jia Qian Wu
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Research Effort ◽  
Reactive Astrocytes ◽  
Sequencing Technologies ◽  
Recent Developments ◽  
Current Therapies ◽  
Pathological Development ◽  
The Many

Alzheimer's disease (AD) is a progressive neurodegenerative disease and is the most common cause of dementia in an aging population. The majority of research effort has focused on the role of neurons in neurodegeneration and current therapies have limited ability to slow disease progression. Recently more attention has been given to the role of astrocytes in the process of neurodegeneration. Specifically, reactive astrocytes have both advantageous and adverse effects during neurodegeneration. The ability to isolate and depict astrocyte phenotype has been challenging. However, with the recent development of single-cell sequencing technologies researchers are provided with the resource to delineate specific biomarkers associated with reactive astrocytes in AD. In this review, we will focus on the role of astrocytes in normal conditions and the pathological development of AD. We will further review recent developments in the understanding of astrocyte heterogeneity and associated biomarkers. A better understanding of astrocyte contributions and phenotypic changes in AD can ultimately lead to more effective therapeutic targets.

scholarly journals A Deep Dive into Genome Assemblies of Non-vertebrate Animals

2021 ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Ramón Rivera-Vicéns ◽  
Romain Koszul ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Current Knowledge ◽  
Genome Structure ◽  
Deep Dive ◽  
Sequencing Technologies ◽  
Current State ◽  
Animal Diversity ◽  
And Function ◽  
Genome Assemblies ◽  
Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

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