Aureliano Bombarely
#Genobotanist and #bioinformatician interested in #plant_domestication and #evolution. Scientist at IBMCP. Former faculty at LaStatale and VTCals.
- We have done our first @protocolsio.bsky.social. Are you interested about #genome_annotation quality evaluation? We have developed a tool called #GAQET2 (github.com/victorgcb198...) which runs several tools like #AGAT, #BUSCO, and many other tools. You can find it at www.protocols.io/view/structu...
- This week I have the wonderful opportunity to present our results for the @catbiogenoma.bsky.social at the @iec.cat in Barcelona with many students and colleagues that I appreciate and admire. For a #genobotanist like me always amazed me #biodiversity in all its forms. Thanks!!! 🌿🌾🍄🟫🐚🪸🐊🐟🦀🦑🦎🐍🦋🪱🦉
- Day 2 on #BCBGENO2025 course has been focused on the genome assembly, from reads to the contigs. Algorithms, methodologies, programs, a little bit of history and many many exercises... up to 16 different ones exploring short, and specially long read assemblies, from #ONT to #PBHiFi.
- A good HMW DNA extraction can safe you a lot of time during the genome assembly. @tank-silvia.bsky.social (from @irnasa.bsky.social) explained on the first day at #BCBGENO2025 course about #experimental_design, #HMW_DNA extractions, and #DNA_sequencing.
- A Kmer profile can give you a lot of information for your genome before you perform the #genome_assembly. At the end of the first day at the #BCBGENO2025 course, I asked the student to interpret the following #Kmer_profiles for 8 different datasets. Would you be able to make sense of these profiles?
- We have started a new online course #BCBGENO2025 about #genome #assembly, #annotation & #analysis by @csic.es, @bcbhubcsic.bsky.social & @segenetica.bsky.social. Two months with 9 days of 4 hours sessions, and many many activities focused in #skill_development. conexion-bcb.csic.es/microcredenc...
- We close the #biodiversity25 conference with a keynote presentation by Ute Hentschel Humeida about the basis of #sponge #symbiosis. “Life has evolved in a sea of microbes”. Microbial diversity already existed before the diversification of Eukaryotes. Host-microbes symbiosis appeared early in time.
- Metaorganism or holobionts are groups of organisms living together. Sponges are a diverse marine animal phyla either >7500 species. They are wonderful example of microbes symbiosis. They are efficient filter feeders and “big bags with pipes connected by jelly. The jelly has many symbiotic bacteria”.
- Sponges are exceptional reservoirs of microbial diversity. Sponges have 4 specific microbial clusters. They have many nitrogen-assimilation and carbon-assimilation bacteria and chemical defenses and defense against external DNA. One example is the Poribacteria phylum specific to sponge.
- Sam Speak closes the session at the #biodiversity25 with a presentation about #tilapia and the gene positive #selection for saline environments. There are 70 tilapia species with variation in saline tolerance. They sequenced several genomes within this group finding twelve positive selected genes.
- Beam Danneels continues at the #biodiversity25 with a presentation about resistant chemical pollutants and induced defenses in #marine_mammals (#chemical_defensome, Chad). Cetaceans lost 2 keys TF involved in the ChD. They have developed a different path. Comparative genomics gave us some insights.
- Ashwini V. Mohan follows at the #biodiversity25 presenting about the #limbless Layard’s snake skink. Snakes and caecilians lost their limbs due variations in one gene, but limbless #lizards have multiple evolutionary paths. They sequenced the Nessia layardi genome (1.55Gb) native to SriLanka.
- Amanda Gardiner follows at the #biodiversity25 with a presentation about #genetic_diversity in sharks, rays and other vertebrates. She analyzed ROH, homozygous regions in vertebrates genomes produced by the VGP. Critically endangered species have more frequently long ROH than other species.
- Niklas Wahlberg opens last day session at the #biodiversity25 with a wonderful presentation about diversification in #Lepidoptera. More than 1000 Lepidoptera #genomes have been sequenced! Some families have more than 100 reference genomes. They have been able to learn many things from them.
- 1- Lepidoptera derives from 32 ancestral linkage groups. 2- Two new gene families have been identified conserved across all the species. About Noctuidae (#moths), 220 genomes have sequenced. They are important nocturnal pollinators. They are also destructive agricultural pests. They have 4 clades.
- Noctuidae taxonomy was messy until several years ago. BUSCO genes from these sequenced genomes helped to resolve the taxonomy. They have highly syntenic genomes either 31 chromosomes. Some lineages have TEs expansions making their genomes bigger.
- Reposted by Aureliano BombarelyStarting tomorrow, broadcast online: #Genomics for #Biodiversity Conference - from #genomes to impact ... join us! www.erga-biodiversity.eu/post/genomic...
- Simona Buonanno closes the 2nd day session at #biodiversity25 presenting benthic genomes in #ascidians. Botryllus schlosseri is a #species_complex. They sequenced 9 ascidian species, including 2 clades of B. schlosseri. BUSCO was higher than 90% for all the genomes.
- Elisa Ramos brings us a presentation about #gulls at the #biodiversity25. The large white-headed gulls lineage has one of the faster #radiation processes of the birds of the northern hemisphere. LarOmics project aims to elucidate the genetic base of the gull #evolution.
- Callum Thomas follows in the afternoon session at #biodiversity25 talking about the development of a #black_soldier_fly #pangenome. They can be used to produce protein for animals feeding. They can be fed by food waste. They are building a pangenome with individuals from different populations.
- Camilla Mazzoni follows at the #biodiversity25 with a presentation about #sloths. Analysis of these genomes revealed that sloths have the higher content of LTR/copia in mammals, some impacting metabolic mitochondrial genes. Genomic studies can help to implement more efficient conservation actions.
- Claire Merot opens the afternoon session at the #biodiversity25 with a presentation about the structural genetic diversity across the tree of life. Structural variants (SVs) are in order de magnitude higher than SNPs. TEs accounts for many SVs. SVs are different across different lineages.
- Eniko Kiss closes the symbiosis genomics session at the #biodiversity25 with a presentation about #convergent_evolution. Mycorrhiza symbiosis is a good example of convergent evolution. Gene family analysis failed to find gene gains rather than losses. PCOC & ESL-PSC methods were used to overcome it
- Merce Montoliu brings us a presentation about wonderful #lichens at the #biodiversity25. Lichens are associations between mycobionts (fungi), photobionts (green algae or cianobacteria) and microbiomes. 38 different lichens were sequenced in DToL & ASH. Results show complex multiorganismal scenarios
- Jose V. Lopez follows at the #biodiversity25 presenting about the giant barrel #sponge genome. We are facing massive extinction event in marine reefs so we need to study sponges before they disappear. Sponges have distinctive #symbiotic microbiomes providing important ecosystem services.
- Amjad Khalaf follows the symbiosis genomics session at #biodiversity25 presenting about #microsporidia tetraploid genomes. Most of them are recent autotetraploids. An interesting model of reproduction is proposed with two different paths: sexual and asexual reproduction.
- Symbiosis genomic session at #biodiversity25 begins with a presentation by Mike Sweet about the #coral genome project. The coral reef bleaching is growing at alarming rate reaching 84% this year. By 2030, they may disappear. Some tools have been developed to slow down the process and allow survival.
- Second day at the #biodiversity25 starts either a presentation by Arnau Sebe-Pedros about #cell_types. Cell types are functional and evolutionary units of animal multicellularity. Biodiversity Cell Atlas aims to scale up the application of single cell method across the tree of life.
- Kai Ye closes the first session at the #biodiversity25 presenting about genome architecture evolution derived from 1000 species HiC data analysis. They use zoom-out approach. Checkerboard score (structural complexity) correlates with species complexity.
- Strong global folding like plants, promote gene clusters and plasticity, Animals have weak global folding with high checkerboard scores and drive to compartments. This may drive specialization. Cool presentation!
- Nomar Waminal brings us a plant-based presentation at #biodiversity25 talking about a #crocus pan-repeatome. Crocus has an ancestral WGD prediversification. Then specific lineages have another more recent WGD. Repeats facilitated descending dysploidy and genome size expansion.
- Lewis Stevens continues at the #biodiversity presenting about the programmed DNA elimination (PDE) in #nematodes. It is mostly telo & centromere satellite DNA but five years ago they discovered unexpected PDE (only telomeres) in ascaridids. Sequencing more genome discovered more species with PDE.
- Most genes removed by PDE are unimportant, but there are some with important functions. Elimination sites co-locate with highly recombinant regions.
- Tomas Hron follows at #biodiversity25 with a presentation about #avian evolution and #dot_chromosomes. Ten years ago new “hidden avian” genes appeared like the chicken genome. They are mostly associated to micro and dot chromosomes. Dot chromosomes are repeated-rich and a high gene loss rate.
- Be aware! Dot chromosomes are poorly sequenced by PacBio HiFi so it is recommended to use ONT.
- Aleksandra Bliznina follows at #biodiversity25 with a presentation about the #evolution of the chromosomes in dark-winged fungus gnats. Autosome and GRCs chromosomes vary across different species. 3 genomes wasn’t enough to elucidate de origins of these chromosomes, so they went for 20!
- Aoife McLysaght opens the conference #biodiversity2025 with a presentation about #genome #rediploidization. Hox genes have been classical example of duplicated genes in animals. Plant species have multiple whole genome duplications (WGD). Speciation events close to WGD may look like independent WGDs
- WGD events produces new alleles , no new genes. It is the re-diploidization process the one that produces new genes.
- The “Understanding Life: using largescale biodiversity reference genomes” #biodiversity25 begins. Mark Baxter opens the conference with acknowledgments. Special event will be a quartet playing music inspired by biology.
- Are you jumping into reference genomes? are you looking for a #genome_assembly, #annotation, #analysis online course? We may be able to help. We have a @bcbhubcsic.bsky.social & @csic.es 6ECTS microcredential for you. Pre-inscriptions open until Oct. 14th. conexion-bcb.csic.es/microcredenc...
- Reposted by Aureliano BombarelyAnika in my department is looking for a Phd student on buckwheat stress responses. Maybe this is something for you? #plantjobs www.fz-juelich.de/en/careers/j...
- Roberto Bassi closes the #SOLRUB2025 with an online plenary presentation about nature-based engineering of plant #photosynthesis.
- Austin Hart closes the last session at the #SOLRUB2025 conference with a presentation about #tomato volatiles. There are two main BCAA-derived #volatile pathways in tomato. GWAS on a tomato population revealed 113 QTLs associated to BCAA derived volatiles. They identified several candidate genes.
- Laura Van der Jeucht follows at #SOLRUB2025 with a presentation about how far-red light increases sugar content in #tomatoes. Far-red light exposure changes the plant architecture. Photosynthesis is not affected but the plant increases CO2 consumption. Sugar source content is increased.
- Satya Swathi Nadakuduti follows in the #SOLRUB2025 meeting presenting about a #Rubicaceae species, Mitragyna speciosa, capable of produce #alkaloids with potential pharmaceutical applications.
- Last day at the #SOLRUB2026 starts with a presentation by Antonio Granell from @ibmcp.bsky.social who is presenting about “how biotechnology can help us to design #tomato metabolic profiles”.
- Reposted by Aureliano BombarelyJob Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply! Please repost!
- Pascal Martin follows at the #SOLRUB2025 with a presentation about endopolyploidy in #tomato fruit development. Endoduplication increases transcription. Changes in the chromatin accessibility contribute to ploidy-specific gene expression changes.
- We come back from the coffee break at #SOLRUB2025 meeting with Magdalena Rossi who is presenting about the molecular mechanisms behind #tomato morphogenesis.
- Pratima Debnath closes the #abiotic_stress session at the #SOLRUB2025 meeting with a presentation about heat stress response in #tomatoes. Plants present #thermal_memory which help to survive high temperatures after an adequate priming. She describes some candidate genes associated with this process
- Next speaker at #SOLRUB2025 is Sara Bergonzi which bring us their studies shout #potato cold and freezing tolerance. Usually potato varieties are frost sensitive. They found overlapping QTLs in several chromosomes for cold tolerance with several promising candidate genes.
- Ivo Rieu follows in this morning session at the #SOLRUB2025. He presents about this important topic associated to #climate_change, heat tolerance in #tomatoes. Anther decrease in length with high temperatures reducing fruit-set. Breed new varieties to overcome this problem is needed.
