Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

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mtDNAcombine: tools to combine sequences from multiple studies

BMC Bioinformatics ◽

10.1186/s12859-021-04048-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Eleanor F. Miller ◽

Andrea Manica

Keyword(s):

Sequence Data ◽

Data Extraction ◽

Bayesian Skyline Plot ◽

Model Organisms ◽

Data Sets ◽

Data Handling ◽

Online Database ◽

Genetic Studies ◽

Wide Range ◽

Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

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Quantitative genetics in conservation biology

Genetics Research ◽

10.1017/s001667239900405x ◽

1999 ◽

Vol 74 (3) ◽

pp. 237-244 ◽

Cited By ~ 69

Author(s):

RICHARD FRANKHAM

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Quantitative Genetics ◽

Conservation Biology ◽

Extinction Risk ◽

Outbreeding Depression ◽

Genetic Adaptation ◽

Genetic Management ◽

Captive Populations ◽

Adaptation To Captivity

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.

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Establishing a genomic database for the medicinal plants in the Brazilian Pharmacopoeia

Chinese Medicine ◽

10.1186/s13020-021-00484-5 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Guan-Ru Zhou ◽

Bao-Sheng Liao ◽

Qiu-Shi Li ◽

Jiang Xu ◽

Shi-Lin Chen

Keyword(s):

Medicinal Plants ◽

Medicinal Plant ◽

Chloroplast Genome ◽

Sequence Data ◽

Genomic Data ◽

National Standard ◽

Data Sets ◽

Herbal Drugs ◽

Genomic Database ◽

Brazilian Medicinal Plants

Abstract Background Brazil is exceptionally abundant in medicinal plant resources and has a rich ethnopharmacological history. Brazilian Pharmacopoeia (BP) acts as a national standard that regulates drug quality and has six published editions. Recent genomic approaches have led to a resurgence of interest in herbal drugs. The genomic data of plants has been used for pharmaceutical applications, protecting natural resources, and efficiently regulating the market. However, there are few genomic databases specifically for medicinal plants, and the establishment of a database that focuses on the herbs contained in the BP is urgently required. Methods The medicinal plant species included in each edition of the BP were analyzed to understand the evolution of the Brazilian herbal drugs. The data of 82 plants in the BP were collected and categorized into four sections: DNA barcodes, super-barcodes, genomes, and sequencing data. A typical web server architecture pattern was used to build the database and website. Furthermore, the cp-Gs of the Aloe genus in the database were analyzed as an illustration. Results A new database, the Brazilian Pharmacopoeia Genomic Database (BPGD) was constructed and is now publicly accessible. A BLAST server for species identification and sequence searching with the internal transcribed spacer 2 (ITS2), the intergenic region (psbA-trnH), and the chloroplast genome (cp-G) of Brazilian medicinal plants was also embedded in the BPGD. The database has 753 ITS2 of 76 species, 553 psbA-trnH and 190 genomes (whole genome and chloroplast genome) of 57 species. In addition, it contains 37 genome sequence data sets of 24 species and 616 transcriptome sequence data sets of 34 species and also includes 187 cp-Gs representing 57 medicinal species in the BP. Analyses of the six cp-Gs of three Aloe species identified the variable regions in the cp-Gs. These can be used to identify species and understand the intraspecific relationships. Conclusions This study presents the first genomic database of medicinal plants listed in the latest BP. It serves as an efficient platform to obtain and analyze genomic data, accelerate studies regarding Brazilian medicinal plants and facilitate the rational development on their market regulation.

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Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Comparative and Functional Genomics ◽

10.1002/cfg.156 ◽

2002 ◽

Vol 3 (2) ◽

pp. 132-136 ◽

Cited By ~ 51

Author(s):

Pankaj Jaiswal ◽

Doreen Ware ◽

Junjian Ni ◽

Kuan Chang ◽

Wei Zhao ◽

...

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Biological Information ◽

Model Organisms ◽

Cereal Crops ◽

Data Sets ◽

Genome Database ◽

Plant Parts ◽

Manual Curation ◽

Plant Ontology

Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.

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Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)

PLoS ONE ◽

10.1371/journal.pone.0256861 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0256861

Author(s):

Danielle N. Stringer ◽

Terry Bertozzi ◽

Karen Meusemann ◽

Steven Delean ◽

Michelle T. Guzik ◽

...

Keyword(s):

Sequence Data ◽

Methodological Approach ◽

Cost Effective ◽

Single Copy ◽

Model Organisms ◽

Protein Coding ◽

Genetics Research ◽

Exon Capture ◽

High Uniformity ◽

Multiple Samples

Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.

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Establishing a Genomic Database for the Traditional Medicinal Plants in the Brazilian Pharmacopoeia

10.21203/rs.3.rs-627096/v1 ◽

2021 ◽

Author(s):

GUANRU ZHOU ◽

Baosheng Liao ◽

Qiushi Li ◽

Jiang Xu ◽

Shilin Chen

Keyword(s):

Medicinal Plants ◽

Medicinal Plant ◽

Chloroplast Genome ◽

Sequence Data ◽

Genomic Data ◽

National Standard ◽

Data Sets ◽

Herbal Drugs ◽

Genomic Database ◽

Traditional Medicinal Plants

Abstract BackgroundBrazil is exceptionally abundant in traditional medicinal plant resources and has a rich ethnopharmacological history. Brazilian Pharmacopoeia (BP) acts as a national standard regulating drugs’ quality and has six published editions. Recent genomic approaches have led to a resurgence of interest in herbal drugs. Plants’ genomic data have been used for pharmaceutical applications, protecting natural resources, and efficiently regulating the market. However, there are few genomic databases specifically on medicinal plants, and establishing one focusing on the herbs of BP is urgently needed. MethodsThe BP editions’ medicinal plant species were analyzed to understand the evolution of the herbal drugs in Brazil. A new database, BPGD (Brazilian Pharmacopoeia Genomic Database), was constructed based on a typical web server architecture. A BLAST server for species identification and sequence searching with internal transcribed spacer 2 (ITS2), intergenic region (psbA-trnH), and chloroplast genome (cp-G) of Brazilian traditional medicinal plants was also embedded in BPGD. Data of 82 plants in BP were collected and categorized into four parts: DNA barcodes, super-barcodes, genomes, and sequencing data. Further, the cp-Gs of Aloe genus in the database were analyzed as an illustration.ResultsBPGD (V1.0) has been tested and opened for public users. The database provides a comprehensive set of data, including the description and identification criteria of medicinal plants, and allows sequence-based search using BLAST. The database has 753 ITS2 of 76 species, 553 psbA-trnH and 190 genomes (whole genome and chloroplast genome) of 57 species, and 37 genome sequence data sets of 24 species and 616 transcriptome sequence data sets of 34 species. The data includes 187 cp-Gs representing 57 medicinal species in BP. Analysis of the six cp-Gs of three Aloe species identified the variable regions in cp-Gs, which could be used to identify species and understand the intraspecific relationship. ConclusionsThis study presents the first genomic database for traditional medicinal plants listed in the latest BP. It serves as an efficient platform to obtain genomic data, specifically on medical plants listed in the BP (http://bpgenome.com/).

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Genetic diversity and population structure of Bretschneidera sinensis, an endangered species

Biodiversity Science ◽

10.3724/sp.j.1003.2013.09117 ◽

2014 ◽

Vol 21 (6) ◽

pp. 723-731

Author(s):

Xu Gangbiao ◽

Liang Yan ◽

Jiang Yan ◽

Liu Xiongsheng ◽

Hu Shangli ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Endangered Species

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Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

Biodiversity Science ◽

10.3724/sp.j.1003.2013.09098 ◽

2014 ◽

Vol 21 (5) ◽

pp. 601-609

Author(s):

Wang Deyun ◽

Peng Jie ◽

Chen Yajing ◽

Lü Guosheng ◽

Zhang Xiaoping ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Endangered Species ◽

Rare And Endangered Species ◽

Rare And Endangered

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Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽

10.3390/ani11030899 ◽

2021 ◽

Vol 11 (3) ◽

pp. 899

Author(s):

Fotis Pappas ◽

Christos Palaiokostas

Keyword(s):

Genetic Diversity ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

Cost Effective ◽

Limiting Factors ◽

Phenotypic Traits ◽

Production Volume ◽

High Coverage ◽

Genomic Relationships ◽

Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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