Biodiversity Genomics 2023

Open | Online | Everywhere

October 02-06 2023

[Programme]

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 1

 BG23 exists to make real the vision of the

Earth Biogenome Project

“sequencing life for the future of life”.

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 2

 Biodiversity Genomics 2023 Programme

Biodiversity Genomics 2023 1

Sponsors 4
Biodiversity Genomics 2023 - Registration 5
BG23 Abstract Book 5
Biodiversity Genomics Academy 6
Programme Overview 7
Origins: of the universe, of life, of species, of humanity 8
Biodiversity Genomics 2023 Concert 8
Detailed Programme 9
Monday October 2nd Biodiversity Genomics Europe 9
Tuesday October 3rd | Europe and the Americas 11
Wednesday October 4th | Africa and Europe 16
Thursday October 5th | Australasia and East Asia 19
Friday October 6th | EBP project and community meetings 21

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 3

Sponsors
Biodiversity Genomics 2023 is brought to you through the generous sponsorship of
PacBio and Arima.

BG23 is funded by The Wellcome Sanger Institute Tree of Life programme and by the
Biodiversity Genomics Europe project.

The BG23 meeting was only possible because of the hard work of the delivery team of
Anushka Mittal, Manuel Batista, Luke Lythgoe and Camila Muyo (Tree of Life,
Wellcome Sanger Institute), Rebecca Loffman (Wellcome Connecting Science) and
Chris Watson (and team, VenueAV).

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 4

Registration is open and will be open through the meeting.

Biodiversity Genomics 2023 - Registration

Once you have registered you will be sent instructions to get into the meeting portal.

Once in the portal, the abstract book is available at

BG23 Abstract Book

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 5

 Biodiversity Genomics Academy
The Biodiversity Genomics Academy ran from 01 September to 29th September 2023.

There were 40 presented workshops with over 1200 participants, covering topics from
read set analysis to genome browsing, via k-mers, assembly, annotation and deep
analysis.

The BGA23 website holds links to the presentations, the GITPOD tutorials and more for
all these amazing “How do you do that” presentations.

BGA23 Website

The presentation recordings are live on the BGA YouTube channel at

BGA YouTube Channel

BGA23 was delivered by Sujai Kumar (Tree of Life, Wellcome Sanger Institute) in
collaboration with a host of workshop presenters, and was enabled through the vision and
generosity of the GitHub developers, who provided space and compute for free. BGA was
managed by Mark Blaxter (Tree of Life, Wellcome Sanger Institute) and core funded from
the Wellcome Sanger Institute.

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Programme Overview

Biodiversity Genomics 2023 | Open. | Online. | Everywhere. Programme Page 7

 Origins: of the universe, of life,
of species, of humanity

Biodiversity Genomics 2023 Concert

On Wednesday and Thursday we are honoured to be able to invite you to a broadcast of
the premiere performance of “Origins”. Origins is a choral oratorio that takes us from the
origins of the universe to our common present and future.

Professor Jenny Graves, who has an illustrious career in

biodiversity genomics research and is an inspiration to our
community, was the prime mover behind this work, and
wrote the libretto.

We are grateful to The Heidelberg Choral Society and

Orchestra (conductor Peter Bandy and director Geoffrey
Grinton) and all their colleagues for this unique
opportunity. The libretto of Origins was written by Jenny
Graves and Leigh Hay, and the music was composed by
Nicholas Bruc. The projected visuals were composed by
Drew Berry (and colleagues at wehi.tv).

The recording is from the world premiere of Origins in the

Melbourne Recital Centre, Australia, on July 18th 2023.

We will broadcast Origins on Wednesday 04th October (Parts III and IV) and Thursday 05th
October (Parts I and II). The performance will only be available “live” during the meeting and will not
be part of the recorded archive of BG23, so don't miss it!.

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Detailed Programme

Monday October 2nd

Biodiversity
Genomics Europe

Time of First name Last name Talk title

talk
BST

Biodiversity Genomics Europe Introduction

09:00 - Gilles Doignon EU and the Global Biodiversity Framework, a new
09:50 chapter thanks to genomic science
Dimitris Koureas Biodiversity Genomics Europe Project: Organising a
systemic solution for scaled-up impact delivery.
Peter Hollingsworth Biodiversity Genomics Europe: DNA barcoding
Camila Mazzoni Biodiversity Genomics Europe: Genome sequencing

Applications: using DNA sequencing to understand and

conserve biodiversity 1
10:00 - Robert Waterhouse Chair
11:15
Kay Lucek Towards a genomic resolution of the Phengaris alcon
species complex
Jacob Höglund Conservation Genomics of the endangered Green Toad
in Sweden
Sarah du Plessis Genomics reveals complex population history and
unexpected diversity of Eurasian otters (Lutra lutra) in
Britain relative to genetic methods
Ana Tavares Reference-free analyses provide insights into the
population genomics of six octocorals
Will Nash Genomic implications of range shifts in hymenopteran
species
Michal Rendoš First insight into molecular diversity and DNA barcode
library of epikarst-dwelling invertebrates in the Western
Carpathians

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Applications: using DNA sequencing to understand and
conserve biodiversity 2
11:45 - Mara Lawniczak Chair
12:45
Vanessa Mata DNA metabarcoding as a tool for improving the
knowledge of nocturnal flying insect communities
Ethan Ross Developing DNA Barcode Reference Libraries using
Oxford Nanopore Sequencing for Monitoring Scottish
Seagrass Biodiversity
Tom Wilding Monitoring environmental impact using bacterial
metabarcoding
Tomasz Rewicz DNA barcode-based survey documents underestimated
diversity and intricate phylogeographic patterns of
aquatic Heteroptera in an endangered Balkan
biodiversity hotspot: ancient Lake Skadar basin
Natasha de Vere Unravelling plant-pollinator interactions using pollen
DNA metabarcoding

Opportunities for increased utilisation of genomic data for biodiversity

characterisation and conservation - presentations catching
technological innovations and logistical opportunities
13:00 - Camila Mazzoni Chair
14:30
Mara Lawniczak DNA barcoding for long term pollinator biomonitoring
Rudolf Meier High-throughput species discovery with robotics and
ONT
Elizabeth Clare Monitoring biodiversity from airborne DNA
Martin C. Fischer Monitoring genetic diversity: a genomics-based pilot
study for Switzerland
Cock van Oosterhout From genomes to conservation

Panel discussion
15:00 - Peter Hollingsworth Panel discussion
16:00 - what do we need to do
Magda Bou Dagher
Kharrat – to make meaningful progress
– to maximise impact of major biodiversity
Tiina Laamanen
genomic projects in meeting stakeholder needs
Charlotte Germain-Aubrey
Michael Traugott
Elena Buzan
Pedro Beja

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Tuesday October 3rd | Europe and the Americas
Time of First name Last name Talk title
talk BST

Welcome
11:00 - Mark Blaxter Welcome
12:00
Harris Lewin Toward 150,000 Reference Genomes

Genomics Technologies 1
Technologies for coordination, generation and analysis of genomes at scale
12:00 - Caroline Howard The wet-lab processes behind 1000 genomes
13:00
Katja Reichel Share it or miss it: Reporting gDNA quality
Bethan Yates A platform for automated creation of Genome Notes
Balázs Bálint Sensitive detection and removal of contamination from
annotated genomes by ContScout
Eric Edsinger Accessible genomes full of potential: Optimizing short-read
reference-guided genome assembly by Zanfona for over 100
diverse multicellular marine eukaryotes from the Salish Sea
(Pacific Northwest, North America).
Donat Agosti Taxon names key to knowledge and reproducibility

Biodiversity Genomics (Europe) 1

13:00 - Dominic Absolon Multi-haplotype curation for high ploidy level plant genomes
14:00
Ole Kristian Tørresen Status and approaches of the Earth BioGenome Project
Norway
Tim Barraclough Comparative genomics of bdelloid rotifers
Sam Ebdon Selection on the Symphypleonan sex chromosomes
Murat Tugrul Evolution of Nuclear Receptor Protein Sequences and DNA
Binding Features in Crustacean Genomes: A Case Study of
the NR2B Family
Vidya Vuruputoor Crossroads of assembling a Moss genome: navigating
contaminants and horizontal gene transfer in
Physcomitrellopsis africana

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Tuesday October 3rd | Europe and the Americas
Time of First name Last name Talk title
talk BST

Biodiversity Genomics (Europe) 2

14:00 - Julia Lopez Evolutionary genomics of the Galápagos iguanas
15:00 Delgado
Giulia Campli Tracing the evolutionary history of moulting genes across
arthropod diversity
Jonathan Ashworth Wildflower genomics to inform the creation of new habitats
Dorine Merlat Annotation of Myriapoda genomes with a new tool: EXOGAP
Rui Alves An almost chromosome-level assembly and annotation of the
Alectoris rufa genome
Wu Huang Using nuclear genome for plant species identification

Chromosomes in Plants, Animals and Protists

15:00 - Pablo Gonzalez De The hidden germline genome of A. rhodensis
16:00 Manuel la Rosa
Aurora Ruiz-Herrera Unveiling patterns of 3D chromatin folding across the
vertebrate phylogeny - insights into genome evolution
Brandon Pickett Telomere-to-telomere ape sex chromosome assemblies
unravel rapid evolution on the Y and conservative evolution on
the X
Aleksandra Bliznina Extreme genome scrambling in cryptic Oikopleura dioica
species
Jorge Duitama A phased genome assembly of a Colombian Trypanosoma
cruzi TcI strain and the evolution of gene families
Christopher Benson Transposable elements play a key role in intraspecific
variation in genome size and chromosome architecture in
allotetraploid Poa annua

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Tuesday October 3rd | Europe and the Americas
Time of First name Last name Talk title
talk BST

Bats1K
16:00 - Emma Teeling Introduction
17:00
Sonja Vernes Introduction
Juan Vazquez Evolution of Non-Allometric Longevity in a Clade of
Long-Lived Bats Resolved Using Chromosome-Length
Genome Assemblies
Karen Sears Insights into the formation and diversification of a novel
chiropteran wing membrane from embryonic development
Orly Razgour Using genomics to understand bat responses to global change
Zixia Huang Comparative genome microsynteny illuminates the fast
evolution of nuclear mitochondrial segments (NUMTs) in
mammals
Amanda Vicente Serum proteomics reveals a tolerant immune phenotype
Santos across multiple pathogen taxa in wild vampire bats
Denis Larkin How Does an Extreme Climate Make Domestic and Wild
Animals Evolve Similarly?

Keynote
17:00 - Animal genome "architecture": measurements and
18:00
Oleg Simakov
function?

SPONSOR TALKS: PacBio

18:00 - Jonas Korlach Long-read sequencing for biodiversity and conservation, at
19:00 scale, with PacBio
Jacob Brandenburg Long-read sequencing for biodiversity and conservation, at
scale, with PacBio

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Tuesday October 3rd | Europe and the Americas
Time of First name Last name Talk title
talk BST

North American BioGenome projects - CCGP and CanBP

19:00 - Michelle Neitzey Implementation of a cohort-based conservation genomics
20:00 student training program
Samantha Jones The Canadian BioGenome Project
Brad Shaffer The California Conservation Genomics Project: Updates and
Progress
Erik Enbody High-throughput comparative population genomics using
comparative migration surfaces across California’s wildlife
Solenne Correard Canadian Earth Biogenome project assembly pipeline
Krzysztof Kozak California Conservation Genomics Project: Next-generation
(Chris) landscape genomics helps protect Pocket Mice and other
endangered life.
Anne Chambers Individual-based landscape genomics for the CCGP

Biodiversity Genomics in Evolution and Conservation 1

20:00 - Rachel Turba Parallel evolution of the unarmored condition in southern
21:00 California threespine stickleback
Igor Ovchinnikov Paleogenomics of Holocene bison in the Northern Plains
Kate Castellano Genomic signatures of exceptional longevity and negligible
aging in the long-lived red sea urchin
Andrew Sharo Despite billions of domesticated trout released in California,
little impact on population genetics of imperiled steelhead trout
Gina Garzon Diving into Peach Palm Diversity: Multi-Strategic Approach
Alessandra Martinez
Fernanda Teixeira Identification of first outliers SNPs of spinner dolphin (Stenella
longirostris) associated with environmental variables in
Western South Atlantic
Avneet Chhina Do genome-wide SNPs and putatively adaptive SNPs identify
the same set of distinct populations?

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Tuesday October 3rd | Europe and the Americas
Time of First name Last name Talk title
talk BST

Biodiversity Genomics in Evolution and Conservation 2

21:00 - Jacopo Martelossi High within- and between-individual structural variability is
22:00 related to transposable element insertions and deletions in
oysters
Jessica Ody De novo whole genome assembly of the Melampus species
complex
Ursula Oggenfuss Co-option of transposable elements across the fungal
kingdom
Jared Bernard What can genomes tell us about the breadth of a species’
hosts?
Aurélien De Jode Assembling the new reference genome of Littorina saxatilis
Antonio Di Meglio Evolutionary history and replication dynamics of RTE-BovB
LINEs in Stylommatophora (Gastropoda)

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Wednesday October 4th | Africa and Europe
Time of First name Last name Talk title
talk BST

African BioGenome Project

08:00 - Bob Kreiken Just and inclusive digitalization of the African biodiversity
09:00 commons
Soumia Ayed MorphoBiometric characterization and genetic biodiversity
of Local Chicken in Algeria
Faten Filimban Complete chloroplast genomes of two mint species
(Lamiaceae) from Al-Madinah, Saudi Arabia: phylogenetic
and genomic comparative analyses
Petra Korlevic WGS of historic Anopheles gambiae mosquitoes
Joachim Nwezeobi Genomic signals of selection in Anopheles funestus
Farooq Omar Al-Ajli Genomic, genetic and phylogenetic evidence for a new
falcon species using chromosome-level genome assembly
of the gyrfalcon and population genomics

Vertebrate Genomes (Europe)

09:00 - Amy Denton Wet lab approaches for the generation of chordate
10:00 reference genomes for the Darwin Tree of Life/Vertebrate
Genomes Project.
Katherin Eliana Otalora Phylogeographic processes and adaptation genetics of the
Alejandra Acevedo endemic lizard Podarcis lilfordi (Günther, 1874) from the
Balearic Islands
Daniele Battilani A genomic perspective on wolf-dog hybrid potential
adaptation to anthropic environments.
Jan Petružela Secondary contacts of hosts and parasites. Detecting
barriers and introgressions using a genome polarisation
method (diem)
Chiara Bortoluzzi The genomic footprint of a recent demographic decline in
the European bison genome
Theodore Squires Ecological Genomics of Rock Ptarmigan in Iceland

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 Wednesday October 4th | Africa and Europe
Time of First Last name Talk title
talk name
BST

Meio- and Micro-Eukaryotes

10:00 - Claudia Weber Accelerated evolution in parasitic cnidarians?
11:00
Erna King Single nematode genomes fill gaps in the phylogeny
Amjad Khalaf Ex-Sporing long-read microsporidian genomes: polyploidy & structural
rearrangements
Samuel Abalde Insights into acoelomorph evolution from the first nemertodermatid
genome
Sergio Avila-Calero Methodological and conceptual development towards truly referencing
the genomes of all biodiversity – The Dark Taxa example
Guifré Torruella The genome of Singekia montserratensis, an apusomonad
heterotrophic flagellate with a pivotal evolutionary position

Concert
11:00 - Origins: of the universe, of life, of species, of humanity
12:00

SPONSOR TALKS: PacBio and Arima

12:00 - Jonas Korlach Long-read sequencing for biodiversity and conservation, at scale, with
13:00 PacBio
Jacob Brandenburg Long-read sequencing for biodiversity and conservation, at scale, with
PacBio
Anthony Schmitt Beyond Assembly: The Role of Hi-C in Comparative Genomics

Symbiosis Genomics
13:00 - Ferran Palero Bacterial endosymbionts of a unique planthopper (Hemiptera:
14:00 Fulgoroidea)
Ute Hentschel Aquatic Symbiosis Genomics: using comparative genomics to reveal
ancient principles underlying sponge-microbe symbioses.
Noah Gettle Advances and Challenges in Symbiotic Systems Genome Assembly
Jay Goldberg Comparative genomics unravel complex coevolutionary relationships in
nature
Camilla Santos Sponges and their symbionts: ASG Project main challenges
Alejandro Llanos In silico detection of antimicrobial peptides in Loripes orbiculatus
Lizcano transcriptome.

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Wednesday October 4th | Africa and Europe
Time of First name Last Talk title
talk BST
name

Justice, Equity, Diversity, and Inclusion + Genomics

14:00 - Marc Palmada Flores A moderated discussion of Justice, Equity,
16:00 Nathaniel Jue
Sadye Paez Diversity, and Inclusion + Genomics
Genomics Technologies 2
16:00 - Damon-Lee Pointon TreeVal: Modernising data generation for curation of chromosome
17:00 & scale genomes
Yumi Sims
Giulio Formenti Kreeq: k-mer-based evaluation of genome assembly consensus
accuracy
Priyanka Surana Unveiling Earth's Biodiversity Tapestry: Empowering Genomics with
FAIR, TRUST, and Open Science Principles
Cibele Sotero-C Using GoaT to Manage Duplication Across Sequencing Initiatives
aio
Emilio Righi The BioGenome Portal, a tool for genomic metadata management
Robert Waterhou A3Cat & ArTraDB: tools for exploring genomic and organismal
se biodiversity
Kamil Jaron GenomeTelescope: Extended genome models for biodiverse
genomes

Genomics Technologies 3
17:00 - Kenji Kojima Repbase: A Comprehensive Database of Eukaryotic Repeat
18:00 Sequences and Transposons
Sina Majidian Orthology inference at scale with FastOMA

Richard Challis BoaT: Interactive genome feature/synteny explorer

Cynthia Webster EASEL (Efficient, Accurate, Scalable Eukaryotic modeLs), a tool for
the improvement of eukaryotic structural and functional genome
annotation
Rich Adams Likelihood-based tests of species tree hypotheses

E. Sally Chang The NCBI Comparative Genomics Resource: Facilitating reliable

comparative genomics analyses for all eukaryotes
James Fleming Scoutknife:

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Thursday October 5th | Australasia and East Asia

Time of First Last name Talk title

talk BST name

Concert
02:00 - Origins: of the universe, of life, of species, of humanity
03:00

SPONSOR TALKS: PacBio and Arima

03:00 - Jonas Korlach Long-read sequencing for biodiversity and conservation, at
04:00 scale, with PacBio
Jacob Brandenburg Long-read sequencing for biodiversity and conservation, at
scale, with PacBio
Anthony Schmitt Beyond Assembly: The Role of Hi-C in Comparative
Genomics

Asian and Australasian BioGenome Projects

04:00 - Tiffany Kosch The Amphibian Genomics Consortium: moving beyond the
07:00 reference genome to increase functional genomics resources
for amphibian ecology, evolution, and conservation
Sunil Sahu The Cycas genome and the early evolution of seed plants
Kumar
Bharat Patnaik Threatened Species Initiative of Korea for biodiversity
Bhusan conservation
Shivakum Manu Exploring biodiversity using extracellular eDNA
ara
Deden Matra RujakBase; a resource for the genome database of
Derajat Indonesian tropical fruits
Kenta Shirasawa Kazusa GP: Genome Project Across All Orders of Angiosperm
Shannon Corrigan The Ocean Genomes Project – A Comprehensive
High-Quality Reference Genome Library for Marine Vertebrate
Conservation and Biodiversity
Reshma Bhasker NGS based approaches to improve conservation efforts in
forest tree species

Break until VGP meeting at 15:00 BST

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Thursday October 5th | Australasia and East Asia
Time of First Last Talk title
talk BST name name

VGP Project meeting

Zoom -
https://hhmi.zoom.us/j/97688170179?pwd=NjJlOFkvMlF4emt5NEh2MjZtenNFZz09
Password: 247852
15:00 - Erich Jarvis Introduction: The VGP and status of Phase 1
18:00
Siavash Mirarab Proposed phylogenetic analyses for Phase 1 VGP species
Jo Wood The good, the bad, and the ugly in genome assembly differences
between species
Benedict Paten Proposed plans for alignments of Phase 1 VGP species
Andreas Pfenning Proposed comparative genomic studies for Phase 1 of the VGP

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Friday October 6th | EBP project and community
meetings
Time of First name Last name Talk title
talk BST

ERGA Structure, Community and Emerging Science

Zoom -
https://unil.zoom.us/j/95749801105
13:00 - Camila Mazzoni Welcome
15:00
Claudio Ciofi

Rob Waterhouse

Torsten Hugo Struck Species selection for genome projects such as ERGA and BGE
– an semi-automated, bottom-up process based on explicitly
defined criteria
Nadège Guiglielmoni Streamlined evaluation of high-quality eukaryote assemblies

Alice Dennis Establishing annotation guidelines for the tree of life

Tom Brown Aligning ERGA with the FAIR Principles for data and metadata -
The IT and Infrastructure Committee
Elena Buzan Engaging stakeholders is crucial for enhancing biodiversity
genomic research in Europe
Klara Eleftheriadi The genome sequence of the Montseny horsehair worm,
Gordionus montsenyensis sp. nov., a key resource to
investigate Ecdysozoa evolution
Barbara Keller A high quality reference genome aids assessing genetic
diversity and conservation of Hottonia palustris in Switzerland
Giulio Formenti The European Reference Genome Atlas: piloting a
decentralised approach to equitable biodiversity genomics

Bats1K community meeting

Zoom -
https://ucd-ie.zoom.us/j/67465871710
15:00 - Emma Teeling Introduction
17:00
Sonja Vernes
Bastian Fromm Accurate microRNA annotation of animal genomes using
trained covariance models of curated microRNA complements
in MirMachine
Graham Hughes Resolving the Laurasiatherian Family Tree: Is Genomics the
Answer?
Daniel Becker Proteomic signatures of SARS-CoV-2 susceptibility in Tadarida

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 brasiliensis
Francisca Cunha Genomic signatures of cold adaptation in bats and other
Almeida mammals
Dominik Schmid Viral, Immunogenetic and genomic diversity in Ghanaian
Hipposiderids
Hannah Frank Bat immunoglobulins: germline and somatic evolution
Hernani Oliveira Unravelling Neotropical bat genomes: challenges and
perspectives

EBP Business Meeting

17:00 - zoom details to be advised to EBP members and affiliates
19:00

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