Chris Armit

Regular readers will know *GigaScience* has published a lot of plant and
animal genomes, and the biggest conference for this research community
is the appropriately named Plant & Animal Genome Conference (PAG). We've
attended a number of these giant meetings at their San Diego base, and
in recent years they have been branching out to host more convenient
satellites in Asia (PAG Asia). Initially organised in Singapore, last
month we went along to PAG Asia as the first time its been hosted on our
doorstep in China. Not as big as the main meeting, [PAG Asia
2019](https://intlpagasia.org/2019/) still had an impressive 354
attendees from 24 different countries. On top of attending in the Futian
Shangri-La, we also participated in one of the workshops, and here is
our write-up of how it went.

> At
> [\#PAGAsia19](https://twitter.com/hashtag/PAGAsia19?src=hash&ref_src=twsrc%5Etfw)
> in Shenzhen for the rest of this week. BGI's Xu Xun is a co-chair of
> the meeting and introducing keynote Ning Yang
> [pic.twitter.com/EG8l2TEt0j](https://t.co/EG8l2TEt0j)
>
> --- GigaScience (@GigaScience) [June 6,
> 2019](https://twitter.com/GigaScience/status/1136456595922071552?ref_src=twsrc%5Etfw)

**DNA Zoo and the \$1000 Genome Assembly  
**With one million species at risk of extinction the is an urgent need
to capture as much genomic data as we can  about these disappearing
species to monitor populations and inform conservation, captive breeding
and re-wilding strategies. Mammalian species are particularly at risk,
with 25% endangered or threatened. This was the rationale of DNA Zoo
workshop that opened the meeting in Shenzhen. While *GigaScience* has
worked with and published many of the outputs of the Genome10K (10,000
vertebrate genomes) consortium that is now focusing on ["platinum-level"
chromosome-scale
genomes](https://www.sanger.ac.uk/news/view/international-vertebrate-genomes-project-releases-first-15-high-quality-reference-genomes)
and constantly testing and throwing together the latest state-of-the-art
genomics technologies, [DNA Zoo](https://www.dnazoo.org/) are aiming at
a slightly different approach. Focusing on a single cost effective
technology (Hi-C) to maximize what they can achieve in the current
limited funding environment. Our recent [African painted-dog
genome](https://doi.org/10.1093/gigascience/giy124) paper that utilized
10X data got close to their \$1,000 ball park de novo genome (costing
roughly \$3,000 USD), and their technological approach will hopefully
bring these costs down further while still providing high-quality
reference genomes. Following our approach at released [bird genomes via
social
media](http://gigasciencejournal.com/blog/a-flock-of-bird-data-comes-to-roost/),
the DNA Zoo team have been releasing their nearly 100 genomic datasets
[via their blog](https://www.dnazoo.org/blog/categories/assemblies).

> Erez saying they've already shared 78 mammalian chromosome scale
> assemblies on <https://t.co/dmYTZe5EA9>. Releasing one genome a week,
> all released without restriction
> [\#PAGAsia19](https://twitter.com/hashtag/PAGAsia19?src=hash&ref_src=twsrc%5Etfw)
> [pic.twitter.com/MUEPp0nLd2](https://t.co/MUEPp0nLd2)
>
> --- GigaScience (@GigaScience) [June 6,
> 2019](https://twitter.com/GigaScience/status/1136480151867252736?ref_src=twsrc%5Etfw)

  
Erez Liberman Aiden of Baylor College of Medicine -- who developed the
Hi-C chromosome conformation capture technique -- delivered the opening
talk for this session and explained how Hi-C, which was primarily
developed for understanding 3D genome architecture, has become a novel,
low-cost solution for delivering a chromosomal level genome assembly.
Hi-C allows locations that were approximate in 3D space to become
adjacent through crosslinking of chromatin. Crosslinked chromatin is
digested into fragments using restriction enzymes, and the crosslinked
fragments are then ligated together. By sequencing these fragments,
researchers obtain a map that helps us understand chromosomal folding in
the nucleus. As Erez points out, the overwhelming finding from these
Hi-C maps is that chromosomes tend to fold on themselves. Indeed, as
Erez explained, "pairs of loci on the same chromosome tend to bump into
each other at a high rate". DNA Zoo have utilised this phenomenon to
develop low-cost chromosomal level genome assemblies. This hybrid
assembly approach uses a combination of Illumina short-read sequences,
which are insufficient for chromosome-level assemblies, combined with
Hi-C data of the same species. Using this approach, the 3D genome maps
inform the sequence assembly at a fraction of the price compared to
using long-read sequencing and/or optical map technology. Olga Dudchenko
-- also from Baylor College of Medicine -- further explained that it was
possible to upgrade a \$1K end-to-end assembly with, for example, PacBio
long reads to produce "platinum assemblies". Olga additionally presented
an overview of the automated pipeline software that DNA Zoo use to
assemble genomes. [Parwinder
Kaur](https://www.dnazoo.org/post/dna-zoo-australia-going-live) of
University of Western Australia further explained how these low-cost
technologies will increase our understanding of genetic biodiversity in
Australia, which includes an astonishing 87% of mammals endemic to the
continent. We are big fans of ["community
genomes"](http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/),
and to get the ball rolling sequencing some of their amazing endemic
wildlife Parwinder has recruited [Chokka the
Quokka](https://www.facebook.com/chokkathequokka/) to crowdfund one of
Australia's [most "selfie-genic"
animals](https://twitter.com/hashtag/quokkaselfie).

::: {#attachment_2946 .wp-caption .alignnone style="width: 810px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2019/06/PAG_Asia_ii.png){.wp-image-2946
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Parwinder Kaur of University of Western Australia explains how Hi-C is
enabling low-cost chromosomal genome assembly, and how this further
impacts on our understanding of genetic biodiversity in Australia.
:::

**Thinking big with 10KP and the Ruili Botanical Garden  
**Gane Ka-Shu-Wong of University of Alberta and BGI-Shenzhen, and Xin
Liu of BGI-Shenzhen introduced the [10,000 Plant Genomes
Project](https://db.cngb.org/10kp/) (10KP, of which we published the
[announcement paper](https://doi.org/10.1093/gigascience/giy013)), which
aims to sequence a vast amount of plant genomes representing every major
clade of plants and eukaryotic microbes. Gane explained that from a
genomics perspective there is a focus on long-range contiguity, and
further highlighted that novel genes found in land plants are also found
in algae, which may suggest that terrestrialization could have begun
with the algae. Gane also reported that preliminary findings from 1KP
([1,000 Plants Project](https://doi.org/10.1186/2047-217X-3-17), of
which we published the [data access
paper](https://doi.org/10.1186/2047-217X-3-17)) suggest an unexpected
abundance of horizontal gene transfer from soil bacteria to algae.
Michael Melkonian of the University of Cologne offered deeper insights
into algae -- and suggested tripartite endosymbiois between
cyanobacteria, *Chlamydia sp.*, and a eukaryotic species as one
possibility for algae's evolutionary origins -- and was quick to point
out that these often overlooked single-cell plants are responsible for
50% of global photosynthesis. Yang Liu of BGI-Shezhen reported on mosses
as a potential source of evolutionary novelties such as the stomata and
cuticle, which are essential for drought resistance. Yang Liu
additionally highlighted the impressive cold and heat resistance traits
that can be found in the *Bryophyta* that allows them to survive in
glaciers and geothermal areas.

> Great to see
> [@Bauhinia](https://twitter.com/bauhinia?ref_src=twsrc%5Etfw) genome
> discussed at
> [\#PAGAsia19](https://twitter.com/hashtag/PAGAsia19?src=hash&ref_src=twsrc%5Etfw),
> Stephen Tsui presenting in the 10KP track on using their data to
> assemble Bauhinia genomes. You can see the slides here
> <https://t.co/foPaScN2eY>
> [pic.twitter.com/dbBEBjD5f3](https://t.co/dbBEBjD5f3)
>
> --- BauhiniaGenome (@BauhiniaGenome) [June 8,
> 2019](https://twitter.com/BauhiniaGenome/status/1137291145547902976?ref_src=twsrc%5Etfw)

  
Huan Liu (BGI-Shenzhen), Stephen Kwok-Wing Tsui (Chinese University of
Hong Kong) and *GigaScience* Executive Editor Scott Edmunds further
reported on the hugely impressive (molecular and imaging) digitization
of the 500-hectare [Botanical Garden in
Ruili](http://gigasciencejournal.com/blog/digital-botanical-garden/) in
subtropical Yunnan province in China. You may have [read the recently
published research](https://doi.org/10.1093/gigascience/giz007), and
this talk provided behind the scenes insight into how this mammoth
project came about. Scott explains, the 689 vascular plant species
sequenced "effectively triples the number of plant species with
available genome data". The first part of the project from Huan Liu
explained how this provided a nice to investing the feasibility and
technical requirements for "planetary-scale" projects such as the 10KP.
Scott then covered the data management and organisation to make this
data discoverable and re-usable. The final part was of a downstream user
perspective, Stephen Tsui showing how he could re-use this unassembled
data for the community [Hong Kong Bauhinia
Genome](http://bauhiniagenome.hk/) project [we have been working with
him
on](http://blogs.biomedcentral.com/on-biology/2015/11/24/help-investigate-genetic-mystery-hong-kongs-floral-emblem-bauhinia-flower/).
For more insight you can see the [slides
here](https://www.slideshare.net/GigaScience/pagasia19-the-digitalization-of-ruili-botanical-garden-project-production-curation-and-reuse).

::: {#attachment_2952 .wp-caption .alignnone style="width: 810px"}
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2019](http://gigasciencejournal.com/blog/wp-content/uploads/2019/06/IMG_4728.jpg){.wp-image-2952
.size-full decoding="async" aria-describedby="caption-attachment-2952"
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sizes="(max-width: 800px) 100vw, 800px"}

Scott Edmunds of *GigaScience* explains how the Ruili Botanical Garden
dataset was captured.
:::

**Crop Informatics  
**Ken McNally of IRRI (International Rice Research Institute) introduced
a diverse selection of talks that reported on the current use of
informatics in rice genomics. Star Yanxin Gao of Cornell University
highlighted the Genomic Open-Source Breeding Informatics Tool Portal
that couples genomic information with phenomic data to enhance decision
making in the breeding of staple crops. In addition, Shuhui Song of the
Beijing Institute of Genomics introduced the BIG Data Center's Rice
Variation Database and highlighted its ability to assess reannotation
results as part of its role in the [Information Commons for
Rice](http://ic4r.org) (IC4R). Following this, Dmytro Chebotarov of IRRI
reported on SNP-Seek, which is a web application that enables efficient
querying of large rice genomic datasets, such as the 3,000 Rice Genomes
(Rice3K) data that we previously [published in a Data
Note](https://doi.org/10.1186/2047-217X-3-7). SNP-Seek incorporates
analysis and visualization tools that include a genome browser with SNP,
gene and structural variants tracks, phylogenetics tree and MDS plot
visualizations. The [Rice Galaxy
server](https://doi.org/10.1093/gigascience/giz028) presenting this data
being one of the winners of our ICG Prize last year and [presented by
first author Venice
Juanillas](https://www.youtube.com/watch?v=HWKa3acoDUQ&t=50s) in our
session at the conference (see
[video](https://www.youtube.com/watch?v=HWKa3acoDUQ&t=611s) below). The
democratising potential of this approach was demonstrated previously by
the *GigaScience* team at [International Data
Week](http://gigasciencejournal.com/blog/democratising-data-aocc/) in
Gaborone, Botswana and it was equally well received at PAG Asia 2019.

[PAG Asia 2020](https://intlpagasia.org) is tentatively scheduled for
Shenzhen again, and if we do not see some of you there we will be at the
main PAG in San Diego in January 2020 and likely provide coverage of how
these and other plant and animal genome projects are proceeding.

The post [PAG Asia 2019: Plant and Animal Genomes (with Chinese
Characteristics)](http://gigasciencejournal.com/blog/pag-asia-2019/){rel="nofollow"}
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Regular readers will know
<em>
 GigaScience
</em>
has published a lot of plant and animal genomes, and the biggest conference for this research community is the appropriately named Plant &amp;

Messaggi di Rogue Scholar

PAG Asia 2019: Plant and Animal Genomes (with Chinese Characteristics)