Genomes on a Tree (GoaT): A centralized resource for eukaryotic genome sequencing initiatives

Genomic data are transforming our understanding of biodiversity and, under the umbrella of the Earth BioGenome Project (EBP - https://www.earthbiogenome.org), many initiatives seek to generate large numbers of reference genome sequences. The distributed nature of this work makes coordination essential to ensure optimal synergy between projects and to prevent duplication of effort. While public sequence databases hold data describing completed projects, there is currently no global source of information about projects in progress or planned. In addition, the scoping and delivery of sequencing projects benefits from prior estimates of genome size and karyotype, but existing data are scattered in the literature. To address these issues, the Tree of Life programme (https://www.sanger.ac.uk/programme/tree-of-life/) has developed Genomes on a Tree (GoaT), an ElasticSearch-powered, taxon-centred database that collates observed and estimated genome-relevant metadata—including genome sizes and karyotypes—for eukaryotic species. Missing values for individual species are estimated from phylogenetic comparison. GoaT also holds declarations of actual and planned activity, from priority lists and in-progress status, to submissions to the International Nucleotide Sequence Database Collaboration (INSDC https://www.insdc.org/), across genome sequencing consortia. GoaT can be queried through a mature API (application programming interface), and we have developed a web front-end that includes data summary visualisations (see https://goat.genomehubs.org/). We are currently transitioning this service into the Tree of Life production pipeline. GoaT currently reports priority lists from the Darwin Tree of Life project (focussed on the biodiversity of Britain and Ireland). We are actively soliciting additional data concerning progress and intent from other projects so that GoaT displays a real-time summary of the state of play in reference genome sequencing, and thus facilitates collaboration and cooperation among projects. We are developing standard formats and procedures so that any project can make explicit its intent and progress. Cross referencing to other data systems such as the INSDC sequence databases, the BOLD DNA barcodes resource and Global Biodiversity Information Facility- and Open Tree of Life-related taxonomic and distribution databases will further enhance the system’s utility. We also seek to incorporate additional kinds of metadata, such as sex chromosome systems, to augment the utility of GoaT in supporting the global genome sequencing effort.

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Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽

10.3390/plants8080270 ◽

2019 ◽

Vol 8 (8) ◽

pp. 270 ◽

Cited By ~ 4

Author(s):

Yun Gyeong Lee ◽

Sang Chul Choi ◽

Yuna Kang ◽

Kyeong Min Kim ◽

Chon-Sik Kang ◽

...

Keyword(s):

Plant Species ◽

Genome Sequencing ◽

Reference Genome ◽

Genome Structure ◽

Plant Genome ◽

Sequence Information ◽

Sequencing Analysis ◽

Oxford Nanopore ◽

A Genome ◽

Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

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The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life

Biology Letters ◽

10.1098/rsbl.2019.0867 ◽

2020 ◽

Vol 16 (3) ◽

pp. 20190867 ◽

Cited By ~ 13

Author(s):

Zoe A. Xirocostas ◽

Susan E. Everingham ◽

Angela T. Moles

Keyword(s):

Sex Chromosome ◽

Meta Analysis ◽

Chromosome Morphology ◽

Tree Of Life ◽

The Other ◽

Deleterious Mutations ◽

Male And Female ◽

Fundamental Understanding ◽

Female Longevity ◽

Heterogametic Sex

Many taxa show substantial differences in lifespan between the sexes. However, these differences are not always in the same direction. In mammals, females tend to live longer than males, while in birds, males tend to live longer than females. One possible explanation for these differences in lifespan is the unguarded X hypothesis, which suggests that the reduced or absent chromosome in the heterogametic sex (e.g. the Y chromosome in mammals and the W chromosome in birds) exposes recessive deleterious mutations on the other sex chromosome. While the unguarded X hypothesis is intuitively appealing, it had never been subject to a broad test. We compiled male and female longevity data for 229 species spanning 99 families, 38 orders and eight classes across the tree of life. Consistent with the unguarded X hypothesis, a meta-analysis showed that the homogametic sex, on average, lives 17.6% longer than the heterogametic sex. Surprisingly, we found substantial differences in lifespan dimorphism between female heterogametic species (in which the homogametic sex lives 7.1% longer) and male heterogametic species (in which the homogametic sex lives 20.9% longer). Our findings demonstrate the importance of considering chromosome morphology in addition to sexual selection and environment as potential drivers of sexual dimorphism, and advance our fundamental understanding of the mechanisms that shape an organism's lifespan.

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The contribution of peer trainers to the Tree of Life project for young people living with Type 1 Diabetes: Building community

Clinical Child Psychology and Psychiatry ◽

10.1177/1359104520952812 ◽

2020 ◽

pp. 135910452095281

Author(s):

Lucy Casdagli ◽

Glenda Fredman ◽

Ellie Huckle ◽

Ella Mahony ◽

Deborah Christie

Keyword(s):

Type 1 Diabetes ◽

Young People ◽

Narrative Therapy ◽

Tree Of Life ◽

Life Project ◽

Building Community ◽

Narrative Practice ◽

Collective Narrative

This paper describes the involvement of peer trainers in Tree of Life groups for young people living with Type 1 Diabetes. The approach is informed by narrative therapy and collective narrative practice and principles, where people are seen as separate from problems and the focus is on creating opportunities for people to tell and witness one another’s preferred identity stories. Young people who have participated in a Tree of Life day are invited to join the project as peer trainers who help facilitate, engage group participants, witness their stories and consult to the project. Involving peer trainers also aims to create a community where preferred identity stories can be lived and witnessed. This paper describes the training for peer trainers and the building of community.

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BarleyVarDB: a database of barley genomic variation

Database ◽

10.1093/database/baaa091 ◽

2020 ◽

Vol 2020 ◽

Author(s):

Cong Tan ◽

Brett Chapman ◽

Penghao Wang ◽

Qisen Zhang ◽

Gaofeng Zhou ◽

...

Keyword(s):

Genome Sequencing ◽

Reference Genome ◽

Agronomic Traits ◽

Genetic Research ◽

Pcr Primers ◽

Genomic Variation ◽

Whole Genome ◽

Hordeum Vulgare L ◽

High Coverage ◽

Barley Genome

Abstract Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at http://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: http://146.118.64.11/BarleyVar

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Genome analyses reveal the hybrid origin of the staple crop white Guinea yam (Dioscorea rotundata)

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015830117 ◽

2020 ◽

Vol 117 (50) ◽

pp. 31987-31992

Author(s):

Yu Sugihara ◽

Kwabena Darkwa ◽

Hiroki Yaegashi ◽

Satoshi Natsume ◽

Motoki Shimizu ◽

...

Keyword(s):

Wild Species ◽

Molecular Breeding ◽

Reference Genome ◽

Sex Chromosome ◽

Hybrid Origin ◽

Dioscorea Rotundata ◽

Tuber Crop ◽

Genome Analyses ◽

Staple Crop ◽

Guinea Yam

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.

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A synthetic phylogeny of freshwater crayfish: insights for conservation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0009 ◽

2015 ◽

Vol 370 (1662) ◽

pp. 20140009 ◽

Cited By ~ 24

Author(s):

Christopher L. Owen ◽

Heather Bracken-Grissom ◽

David Stern ◽

Keith A. Crandall

Keyword(s):

Conservation Status ◽

Iucn Red List ◽

Tree Of Life ◽

Rate Variation ◽

Freshwater Crayfish ◽

Life Project ◽

Phylogenetic Studies ◽

Taxonomic Framework ◽

Status Data ◽

Synthesis Approach

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project ( opentreeoflife.org ) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts.

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A comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia

10.1101/2021.11.29.470452 ◽

2021 ◽

Author(s):

Iulia Darolti ◽

Pedro Almeida ◽

Alison E Wright ◽

Judith E Mank

Keyword(s):

Sex Chromosomes ◽

Reference Genome ◽

Sex Chromosome ◽

De Novo ◽

Sequence Similarity ◽

Sequence Evolution ◽

Structural Variations ◽

Recombination Suppression ◽

Custom Made ◽

Methodological Approaches

Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here we apply different analytical methodologies to the same dataset to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made de novo genome assemblies for the focal species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.

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Assessment the Quality of Genome Assemblies by using QUAST Tool for Metagenomics

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.e6435.038620 ◽

2020 ◽

Vol 8 (6) ◽

pp. 4253-4259

Keyword(s):

Genome Sequencing ◽

Reference Genome ◽

Assessment Tool ◽

Quality Assessment Tool ◽

Assembly Evaluation ◽

Assembly Algorithms ◽

Genome Assemblies ◽

Modern Tool ◽

Assembly Software

Number of assembly algorithms have emerged out but due to constraints of genome sequencing techniques no one is perfect. Various methods for assembler’s comparison have been developed, but none is yet a recognized standard. The problem of evaluating assemblies of formerly unsequenced species has not been considered, because mostly existing methods for comparing assemblies are only applicable to new assemblies of finished genomes. For comparing and evaluating genome assemblies we have used QUAST (Quality Assessment Tool). This tool is used to assess the quality of leading assembly software by evaluating quality metrics. Assemblies with a reference genome, as well as without a reference can be evaluated by QUAST tool. For genome assembly evaluation based on alignment of contigs to a reference, it is a modern tool. In this study we demonstrate QUAST performance by comparing several leading genome assemblers on three metagenomic datasets.

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Nurturing a sustainable Open Tree of Life

Biodiversity Information Science and Standards ◽

10.3897/biss.2.25727 ◽

2018 ◽

Vol 2 ◽

pp. e25727

Author(s):

Emily Jane McTavish ◽

Mark Holder ◽

Karen Cranston

Keyword(s):

Community Engagement ◽

Evolutionary History ◽

Tree Of Life ◽

Collaborative Effort ◽

Biodiversity Data ◽

Phylogenetic Information ◽

Life Project ◽

Analysis Tools ◽

Ready Access

The Open Tree of Life project is a collaborative effort to synthesize, share and update a comprehensive tree of life Fig. 1. We have completed a draft synthesis of a tree summarizing digitally available taxonomic and phylogenetic knowledge for all 2.6 million named species, available at tree.opentreeoflife.org Hinchliff et al. 2015. . . This tree provides ready access to phylogenetic information which can link together biodiversity data on the basis of what we know about relevant evolutionary history. Both the unified reference taxonomy Rees and Cranston 2017 and the published phylogenetic statements underlying the tree McTavish et al. 2015 are available and accessible online. Taxa in the phylogenies are mapped to the the reference taxonomy, which aligns Open Tree taxon identifiers to those from NCBI and GBIF, among several other taxonomy resources. The synthesis tree is revised as new data become available, and captures conflict and consensus across different published phylogenetic estimates. This undertaking requires both development of novel infrastructure and analysis tools, as well as community engagement with the Open Tree of Life project. I will discuss the challenges in and the progress towards achieving these goals.

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Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

10.1101/2020.07.14.202564 ◽

2020 ◽

Author(s):

Yu Sugihara ◽

Kwabena Darkwa ◽

Hiroki Yaegashi ◽

Satoshi Natsume ◽

Motoki Shimizu ◽

...

Keyword(s):

Wild Species ◽

Molecular Breeding ◽

Reference Genome ◽

Sex Chromosome ◽

Hybrid Origin ◽

Food Crop ◽

Dioscorea Rotundata ◽

Tuber Crop ◽

Genome Analyses ◽

Guinea Yam

AbstractWhite Guinea yam (Dioscorea rotundata) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the wild Dioscorea species using an improved reference genome sequence of D. rotundata. Our results suggest a hybrid origin of white Guinea yam from crosses between the rainforest wild species D. praehensilis and the savannah-adapted D. abyssinica. We identified a higher genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and an extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improvement of this crop through molecular breeding.

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