EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Abstract Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila . We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain. 

https://www.nature.com/articles/s41467-022-35198-1.pdf

Cell type diversity in a developing octopus brain

Soft-bodied cephalopods such as the octopus are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled mRNAs and small RNAs in 18 tissues of the common octopus. We show that the major RNA innovation of soft-bodied cephalopods is a massive expansion of the miRNA gene repertoire. These novel miRNAs were primarily expressed in neuronal tissues, during development, and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, strikingly, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains. One-Sentence Summary miRNAs are deeply linked to the emergence of complex brains.

/pdf/micrornas-are-deeply-linked-to-the-emergence-of-the-complex-2uc80lpg.pdf

MicroRNAs are deeply linked to the emergence of the complex octopus brain

Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains. 

/pdf/micrornas-are-deeply-linked-to-the-emergence-of-the-complex-2686ugfl.pdf

The nautilus, commonly known as a "living fossil," is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of the biology and evolution of nautilus, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and high survival of the nautilus. Besides, we also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of the N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and its closely related species.

Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”

The Cephalopoda are a group of highly diverse marine species in the phylum Mollusca, which are distributed worldwide They have evolved some vertebrate-like biological traits and exhibit complicated behavioural repertoires Thus, they are interesting species for studying the mechanisms of evolutionary convergence, innovational functional structures and evolutionary adaptation to a highly active, predatory lifestyle in diverse marine environments Despite the evolutionary placement and biological significance of cephalopods, genomic data on these organisms remain limited Here, we assembled a chromosome-level genome of a female East Asian common octopus (Octopus sinensis) by combining Pacific Bioscience (PacBio) single-molecule real-time sequencing, Illumina paired-end sequencing and Hi-C technology An O sinensis genome of 272 Gb was assembled from a total of 24501 Gb high-quality PacBio sequences The assembled genome represents 802% completeness (BUSCO) with a contig N50 of 49036 Kb and a scaffold N50 of 10589 Mb, showing a considerable improvement compared with other sequenced cephalopod genomes Hi-C scaffolding of the genome resulted in the construction of 30 pseudochromosomes in Cephalopoda, representing 9641% of the assembled sequences The genome contained 4226% repeat sequences and 5,245 noncoding RNAs A total of 31,676 protein-coding genes were predicted, of which 8273% were functionally annotated The comparative genomic analysis identified 17,020 orthologous gene families, including 819 unique gene families and 629 expanded gene families This genomic information will be an important molecular resource for further investigation of biological function and evolutionary adaptations in octopuses, and facilitate research into their population genetics and comparative evolution

Huilai Shi

Papers

Chromosome-level genome assembly of the East Asian common octopus (Octopus sinensis) using PacBio sequencing and Hi-C technology.