John Lovell
@jotlovell.bsky.social
Helping to make genomics useful for crop improvement, ecology, evolutionary biology, and conservation
HudsonAlpha Genome Sequencing Center and DOE Joint Genome Institute
HudsonAlpha Genome Sequencing Center and DOE Joint Genome Institute
Reposted by John Lovell
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
September 30, 2025 at 2:19 AM
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
Just an outrageous amount of structural variation in pennycress. While not yet reproductively isolated, its likely these shredded pericentromeres contribute to some reproductive incompatibilities.
Whole-genome alignments revealed pennycress has nearly dichotomous genome compartmentalization: huge gene-poor pericentromeric regions (~300Mb; <1% genic) with frequent rearrangements and highly syntenic gene-rich chromosome arms (~150Mb; ~20% genic). What we call a "two-speed" genome structure. 3/
September 29, 2025 at 5:33 PM
Just an outrageous amount of structural variation in pennycress. While not yet reproductively isolated, its likely these shredded pericentromeres contribute to some reproductive incompatibilities.
Reposted by John Lovell
New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/
Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome
Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...
www.biorxiv.org
September 28, 2025 at 5:25 PM
New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/
Reposted by John Lovell
C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]
September 24, 2025 at 8:33 PM
C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]
Reposted by John Lovell
Don't forget to apply to our position in Evolutionary Genetics at U of South Carolina!
In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB!
Review starts in 1 week (Oct 1)!
In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB!
Review starts in 1 week (Oct 1)!
Please repost and amplify !
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina!
Check us out and come be our colleague!
sc.edu/study/colleg...
Deadline for applications is Oct 1
#AcademicJobs #EvoBio
Assistant Professor position in Evolutionary Genetics - Department of Biological Sciences | University of South Carolina
sc.edu
September 24, 2025 at 1:32 PM
Don't forget to apply to our position in Evolutionary Genetics at U of South Carolina!
In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB!
Review starts in 1 week (Oct 1)!
In my experience it is a fantastic place to start a new lab, with friendly and supportive colleagues and many junior faculty in EEB!
Review starts in 1 week (Oct 1)!
Reposted by John Lovell
And yes, now is the right time.
New for @undark.org
"The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago."
undark.org/2025/09/11/o...
New for @undark.org
"The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago."
undark.org/2025/09/11/o...
It’s Time to Rethink the Academic Tenure Process
Opinion | To fight the war on science, higher education needs to reimagine the most important career milestone for faculty.
undark.org
September 11, 2025 at 2:09 PM
And yes, now is the right time.
New for @undark.org
"The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago."
undark.org/2025/09/11/o...
New for @undark.org
"The fundamental problem with the tenure process is that it has struggled to recognize that knowledge is curated, created, and consumed differently today than even a decade ago."
undark.org/2025/09/11/o...
Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
August 18, 2025 at 4:51 PM
Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
Reposted by John Lovell
Motherfucker wrote one sloppy paper in April 2020 and instead of being like oops, shit, my bad, he has kept doubling down until now he's killing most promising medical technology of the past quarter century rather than going to therapy.
August 14, 2025 at 4:30 AM
Motherfucker wrote one sloppy paper in April 2020 and instead of being like oops, shit, my bad, he has kept doubling down until now he's killing most promising medical technology of the past quarter century rather than going to therapy.
This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'.
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Developing future resilience from signatures of adaptation across the sorghum pangenome https://www.biorxiv.org/content/10.1101/2025.08.01.667986v1
August 6, 2025 at 8:32 PM
This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'.
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:
🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Postdoctoral Research Associate - Plant Systems Biology & The Center for Bioenergy Innovation (CBI)
Postdoctoral Research Associate - Plant Systems Biology & The Center for Bioenergy Innovation (CBI)
jobs.ornl.gov
July 21, 2025 at 1:52 PM
🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics
Apply by 18-Aug
Apply here: jobs.ornl.gov/job/Oak-Ridg...
@jrossibarra.bsky.social your kind of street art
May 26, 2025 at 4:29 PM
@jrossibarra.bsky.social your kind of street art
Wow, the cover looks great!
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Check out the beautiful cover to our focus issue on Translational research from Arabidopsis to crop plants and beyond. More articles coming shortly. Congrats Patrice Salome and @jotlovell.bsky.social. @theplantcell.bsky.social academic.oup.com/plcell/issue...
May 14, 2025 at 1:39 PM
Wow, the cover looks great!
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Nice work Patrice and @roederlab.bsky.social
The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome
Reposted by John Lovell
The PLANTS program (funded by NSF) at @botsocamerica.bsky.social was a cornerstone of the conference each year, bringing together new-to-science scholars with more experienced mentors. It helped provide community, support, and connection to new scientists.
The grant was terminated last week.
The grant was terminated last week.
May 13, 2025 at 1:36 PM
The PLANTS program (funded by NSF) at @botsocamerica.bsky.social was a cornerstone of the conference each year, bringing together new-to-science scholars with more experienced mentors. It helped provide community, support, and connection to new scientists.
The grant was terminated last week.
The grant was terminated last week.
Reposted by John Lovell
We begin reviewing applications next week!
April 29, 2025 at 3:57 PM
We begin reviewing applications next week!
Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv.
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding https://www.biorxiv.org/content/10.1101/2025.01.30.635736v1
February 3, 2025 at 9:23 PM
Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv.
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
🧵with some background and a few things we found 👇 bsky.app/profile/bior...
Reposted by John Lovell
My work on a pangenome for the hexaploid oilseed crop Camelina sativa is now out early access in Genetics! This young polyploid genome has a small pangenome to match it's low SNP diversity, but regained lost diversity by packing in all the unique genes from its 3 diploid progenitors.
Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa
Abstract. Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it i
doi.org
November 15, 2024 at 11:35 PM
My work on a pangenome for the hexaploid oilseed crop Camelina sativa is now out early access in Genetics! This young polyploid genome has a small pangenome to match it's low SNP diversity, but regained lost diversity by packing in all the unique genes from its 3 diploid progenitors.
Last week we published a peanut genome that was much more complex than it originally appeared.
A 🧵 about 🥜 genomes and what we found ...
Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....
A 🧵 about 🥜 genomes and what we found ...
Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....
Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar
The genome sequence for the drought tolerant peanut variety
academic.oup.com
November 12, 2024 at 11:05 PM
Last week we published a peanut genome that was much more complex than it originally appeared.
A 🧵 about 🥜 genomes and what we found ...
Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....
A 🧵 about 🥜 genomes and what we found ...
Find the article as a ‘featured’ genome report in G3: academic.oup.com/g3journal/ar....
Reposted by John Lovell
Genomics, evolution, and more starter pack!
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
November 10, 2024 at 8:27 PM
Genomics, evolution, and more starter pack!
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
Help build community with this starter pack.
This list is currently incomplete. Want to be included? Reply and I will remedy that!
go.bsky.app/JjvzkWU
@carlbergstrom.com you had a post about making 🐦⬛ friends a while back - mind linking it here? We’re gonna try it out with the magpies on our street. Got the 🥜 ready to go
November 12, 2024 at 12:19 AM
@carlbergstrom.com you had a post about making 🐦⬛ friends a while back - mind linking it here? We’re gonna try it out with the magpies on our street. Got the 🥜 ready to go
Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...
March 29, 2024 at 5:14 PM
Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...
Reposted by John Lovell
The All of Us paper is rightly being criticized for its UMAP figure, which suggests an overly discrete view of human variation—a problem that is compounded by colouring the plot with self-identified race and then omitting the “self-identified” from the title & legend. 1/n
February 21, 2024 at 5:12 AM
The All of Us paper is rightly being criticized for its UMAP figure, which suggests an overly discrete view of human variation—a problem that is compounded by colouring the plot with self-identified race and then omitting the “self-identified” from the title & legend. 1/n
Reposted by John Lovell
I can confirm the appalling news that Duke intends to close its 800K specimen herbarium as part of an embarrassing plan to delete its position as a leader in biodiversity research. This is despite successful fundraising efforts with a donor secured to save the herbarium.
February 15, 2024 at 2:44 AM
I can confirm the appalling news that Duke intends to close its 800K specimen herbarium as part of an embarrassing plan to delete its position as a leader in biodiversity research. This is despite successful fundraising efforts with a donor secured to save the herbarium.
Excellent postdoc right at the cutting edge of genomics; the Harkess lab is great!
“collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.”
hudsonalpha.applicantpro.com/jobs/3238779
“collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.”
hudsonalpha.applicantpro.com/jobs/3238779
February 14, 2024 at 1:11 AM
Excellent postdoc right at the cutting edge of genomics; the Harkess lab is great!
“collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.”
hudsonalpha.applicantpro.com/jobs/3238779
“collab w/ Loren Honaas (USDA) & Stephen Ficklin (WSU) labs to sequence 1000s of apple/pear RNAs to develop biomarker assays for maturity and post-harvest traits. $60,000.”
hudsonalpha.applicantpro.com/jobs/3238779
🚨We're hiring🚨
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
HudsonAlpha - Staff Scientist - Genome Sequencing Center - Huntsville, AL
Position: STAFF-SCIENTIST: Evolutionary gen
hudsonalpha.applicantpro.com
January 30, 2024 at 5:37 PM
🚨We're hiring🚨
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389
We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.
Pls share!
hudsonalpha.applicantpro.com/jobs/3211389