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...
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.
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”.
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.
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.
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.
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.
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.
Starting 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.
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!
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.
