Scott Edmunds

*![1KP capstone
data](http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig1-300x258.jpeg){.wp-image-3110
.alignright loading="lazy" decoding="async" width="254" height="218"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig1-300x258.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig1-768x661.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig1-1024x882.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig1.jpeg 1887w"
sizes="(max-width: 254px) 100vw, 254px"}**Lessons learned in the
evolution of large-scale data sharing**  
New studies out today elucidate* *the framework for 1 billion years of
green plant evolution. The work are the results of nearly a decades work
from an international consortium of nearly 200 plant researchers*
*generating gene sequences from more than 1100 plant species. Here and
in an accompanying Data Note on the 1KP capstone data we provide a
behind-the-scenes look at how this was carried out.*

The 1KP: [[One Thousand Plant Transcriptomes
Initiative](https://sites.google.com/a/ualberta.ca/onekp/)]{.underline}
(or [more accurately the
1.2KP](http://www.acgt.me/blog/2014/10/27/data-access-for-the-1000-plants-1kp-project))
is a mammoth effort to examine the diversification of plant species,
genes and genomes across the more than one-billion-year history of green
plants dating back to the ancestors of flowering plants and green algae.
In 2014 the initial pilot based on the phylogenomics analysis of the
first 85 species [was
released](https://doi.org/10.1073/pnas.1323926111), and accompanying
this [we published](https://doi.org/10.1186/2047-217X-3-17) a useful
guide for the data access for the ongoing project. Recent decades have
seen the [rise of these "mega-sequencing"
projects](https://www.huffpost.com/entry/sequencing-genomes-life_b_7036550),
and in 2009 the Toronto Data Release Workshop affirmed the commitments
to prepublication release of large genomic data sets which were
originally developed in Human Genome Project. The resulting [Toronto
Statement](https://www.nature.com/articles/461168a) encouraged data
producers to produce a citable statement in which they describe the data
set and their intentions in respect of analysis and publication. The
original *GigaScience* paper filled that requirement, linking to the
treasure trove of raw and processed data that supported the project that
have been building in the
[EBI](https://www.ebi.ac.uk/ena/data/view/PRJEB4922),
[Cyverse](http://dx.doi.org/10.25739/8m7t-4e85), and our [GigaDB
repository](https://doi.org/10.5524/100627).

Five years on its nice to see this project on to its conclusion with the
[capstone analysis in
*Nature*](https://www.nature.com/articles/s41586-019-1693-2), and an
accompanying [*GigaScience* Data
Note](https://doi.org/10.1093/gigascience/giz126) again describes the
whole data set and provides additional details on the sample and
sequence processing as well as quality assessments of the 1KP capstone
data. Adding value by providing a user guide for data re-use, [links to
detailed protocols](http://dx.doi.org/10.17504/protocols.io.439gyr6)
(thanks to protocols.io for their help in inputting the 18 different
RNA-extraction methods in), and a lot of other behind-the-scenes
information. like the contamination analysis. These details are useful
for the box-set completists and data re-users, rather than the casual
readers of the capstone paper that are only interested in the narrative.

This narrative fascinating though in throwing light on the complicated
and billion year journey of the evolution of plants. The findings in
*[[Nature](https://www.nature.com/)]{.underline}*, reveal the complex
timing of whole genome duplications and the origins, expansions and
contractions of gene families contributing to fundamental genetic
innovations enabling the evolution of green algae, mosses, ferns,
conifer trees, flowering plants and all other green plant lineages. The
history of how and when plants secured the ability to grow tall, and
make seeds, flowers and fruits provides a framework for understanding
plant diversity around the planet including annual crops and long-lived
forest tree species.

The study inspired a community effort to gather and sequence diverse
plant lineages derived from terrestrial and aquatic habitats on a global
scale. Open to everyone, over 100 taxonomic specialists contributed
material from field and living collections that include the [Central
Collection of Algal Cultures](http://www.ccac.uni-koeln.de/), [Royal
Botanic Gardens, Kew](https://www.kew.org/),  [Royal Botanic Garden
Edinburgh](https://www.rbge.org.uk/), [Atlanta Botanical
Garden](https://atlantabg.org/), [New York Botanical
Garden](https://www.nybg.org/), [Fairylake Botanical Garden,
Shenzhen,](http://www.szbg.ac.cn/) The [Florida Museum of Natural
History](https://www.floridamuseum.ufl.edu/), [Duke
University](https://www.duke.edu/), [University of British Columbia
Botanical Garden](https://botanicalgarden.ubc.ca/) and [The University
of Alberta](https://www.ualberta.ca/). Size and scale or participation
and sampling matters. By sequencing and analyzing genes from a broad
sampling of plant species, researchers are better able to reconstruct
gene content in the ancestors of all crops and model plant species, and
gain a more complete picture of the gene and genome duplications that
enabled evolutionary innovations. A decade ago such an ambitious and
multi-participatory project on 1,000 species was very new, and other
than individual genome projects there was little in the way of role
models on how to carry this out. On top of proving a great example of
the way to carry out open and collaborative large-scale research, it
also provided an interesting model of how such work could be supported
outside of traditional funding streams that were starting to lose
interest in (non-clinical) genome projects.

Project instigator Gane Ka-Shu Wong organized private funding through
the Somekh Family Foundation as well as support from the Government of
Alberta and a sequencing commitment from BGI to launch 1KP. Once the
project was operational, additional computational and data storage
resources came from other ongoing projects, including
[CyVerse](https://www.cyverse.org/) (formerly iPlant). The massive scope
of the project demanded development and refinement of completely new
computational tools for sequence assembly and phylogenetic analysis,
including the
[SOAPdenovo-trans](https://doi.org/10.1093/bioinformatics/btu077) *de
novo* transcriptome assembler designed specifically for the project that
has subsequently been a extremely popular tool for many in the RNA-seq
community.

::: {#attachment_3109 .wp-caption .aligncenter style="width: 814px"}
![1KP capstone
data](http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/Gane1KP_SZ-1024x833.jpeg){.wp-image-3109
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3109" width="804" height="654"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/Gane1KP_SZ-1024x833.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/Gane1KP_SZ-300x244.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/Gane1KP_SZ-768x625.jpeg 768w"
sizes="(max-width: 804px) 100vw, 804px"}

Gane Ka-Shu Wong presenting 1KP & 10KP results at the PAG Asia workshop
we participated in.
:::

"New algorithms were developed by software engineers at BGI to assemble
the massive volume of gene sequence data generated for this project,"
explained Wong. With the computational outputs of much of this currently
being written and reviewed as Data Notes in a similar manner to the
[phylogenomic resources](https://doi.org/10.1186/s13742-014-0038-1) we
published alongside the [Avian Phylogenomic
Project](http://avian.genomics.cn/en/), that also aimed to resolve the
phylogeny of major branch of the tree of life ([see
GigaBlog](http://gigasciencejournal.com/blog/a-flock-of-bird-data-comes-to-roost/)).
Some of these are already coming out as pre-prints, for example [this
work in bioRxiv](https://www.biorxiv.org/content/10.1101/735076v1)
covering the whole genome duplications.

Also involved in the [Avian Phylogenomic
Project](http://avian.genomics.cn/en/), Computer scientists [[Tandy
Warnow](https://ece.illinois.edu/directory/profile/warnow)]{.underline}
of the [[University of Illinois](https://illinois.edu/)]{.underline} and
[[Siavash Mirarab](http://eceweb.ucsd.edu/~smirarab/)]{.underline} of
the [[University of California San
Diego](https://ucsd.edu/)]{.underline} developed new algorithms for
inferring evolutionary relationships from hundreds of gene sequences for
over one thousand species, addressing substantial heterogeneity in
evolutionary histories across the genomes.

"Gene family expansions through duplication events catalyzed
diversification of plant form and function across the green tree of
life," said co-author [Marcel
Quint,](https://quintlab.landw.uni-halle.de/) professor of crop
physiology, at [Halle](https://www.uni-halle.de/)
University[,]{.underline} Germany. "Such expansions unleashed during
terrestrialization or even before set the stage for evolutionary
innovations including the origin of the seed and later the origin of the
flower."

"The view of evolutionary relationships provided by 1KP has led to new
hypotheses about the origins of key structures and processes in green
plants," said co-author [Pam
Soltis](https://biodiversity.institute.ufl.edu/about/dr-pamela-s-soltis-director-of-biodiversity-institute/),
of the Florida Museum of Natural History, [University of
Florida](http://www.ufl.edu/).

::: {#attachment_3107 .wp-caption .alignright style="width: 310px"}
![](http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig7-300x267.jpeg){.size-medium
.wp-image-3107 loading="lazy" decoding="async"
aria-describedby="caption-attachment-3107" width="300" height="267"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig7-300x267.jpeg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig7-768x684.jpeg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig7-1024x912.jpeg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/10/giy013fig7.jpeg 1654w"
sizes="(max-width: 300px) 100vw, 300px"}

Understanding the huge diversity of protists is one of the focuses of
the follow on 10KP project. Source 1KP doi:10.1093/gigascience/giy013
:::

**From 1K to 10K (and beyond)**  
With the 1KP reaching its conclusion, many of the team are now scaling
up to whole genomes and larger sample sizes with the 10KP project that
we [published an
announcement](https://doi.org/10.1093/gigascience/giy013) paper on last
year. This aims to sequence complete genomes from more than 10,000
plants and protists, and address fundamental questions in plant
evolution and diversity. Building an annotated reference genome for a
member of every genus of the land plants and green algae, as well as a
phylodiverse set of species representing both photosynthetic and
heterotrophic protists.

With even bigger challenges regarding taxonomic sampling and collection
for 10KP, a pilot of this was carried out to provide insight into the
feasibility and technical requirements for such "planetary-scale" genome
projects. This was the [digitization of Ruili botanical garden genome
project](http://gigasciencejournal.com/blog/digital-botanical-garden/)
that [we published](https://doi.org/10.1093/gigascience/giz007) earlier
this year, and presented on with many of the 1KP and 10KP consortium in
a workshop at the PAG Asia meeting in June (see above picture and
[GigaBlog](http://gigasciencejournal.com/blog/pag-asia-2019/)). Watch
this space on the continuing legacy of this work, and see how the
offspring of 1KP and other large scale phylogenomics projects covering
other corners of the tree of life continues to bear fruit. For more on
this project see the 1KP website
([www.onekp.com](http://www.onekp.com)), where information on the
continued outputs is being catalogued and collected.

### ** References** {#references}

Carpenter et al. Access to RNA-sequencing data from 1,173 plant species:
The 1000 Plant transcriptomes initiative (1KP). *Gigascience*. 2019.
doi:[10.1093/gigascience/giz126](https://doi.org/10.1093/gigascience/giz126)

One Thousand Plant Transcriptomes Initiative. One thousand plant
transcriptomes and the phylogenomics of green plants. *Nature*,
**574**:2019, doi:
[10.1038/s41586-019-1693-2](https://www.nature.com/articles/s41586-019-1693-2)

Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM,
Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham
SW, Soltis PS,  Liu X, Xu X, Wong GK. 10KP: A phylodiverse genome
sequencing plan. *Gigascience*. 2018 Mar 1;**7**(3):1-9. doi:
[10.1093/gigascience/giy013](https://doi.org/10.1093/gigascience/giy013).

The post [Harvesting the final fruits of the plant tree of
life](http://gigasciencejournal.com/blog/1kp-capstone-data/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


Lessons learned in the evolution of large-scale data sharing
 
 New studies out today elucidate


 the framework for 1 billion years of green plant evolution. The work are the results of nearly a decades work from an international consortium of nearly 200 plant researchers


 generating gene sequences from more than 1100 plant species.

Rogue Scholar Beiträge

Harvesting the final fruits of the plant tree of life