頭足類のゲノム関連の論文が近年連続して出ているので，メモ．
今後ますます発展していく分野になると思うので，しっかり追っていきたい．
リファレンス-1
Genome and transcriptome mechanisms driving cephalopod evolution.
Albertin, C. B., Medina-Ruiz, S., Mitros, T., Schmidbaur, H., Sanchez, G., Wang, Z. Y., ... & Rokhsar, D. S. (2022). Nature communications, 13(1), 2427.
https://doi.org/10.1038/s41467-022-29748-w
要旨-1
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.
ヤリイカの仲間である Doryteuthis (Loligo) pealeiiのゲノムを読み，染色体レベルでアセンブリを行った論文．ゲノムの構造に注目し， Octopus bimaculoides (カリフォルニアツースポットダコ) や Euprymna scolopes (ハワイミミイカ) についても染色体レベルで解析し直して比較を行っている．RNA edittingの機構にも注目しているグループなので，各組織のトランスクリプトーム解析も並行して行い，RNA edittingが各組織でどの程度見られるのか、にも着目して解析を行っている．
リファレンス-2
Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization.
Schmidbaur, H., Kawaguchi, A., Clarence, T., Fu, X., Hoang, O. P., Zimmermann, B., ... & Simakov, O. (2022). Nature communications, 13(1), 2172.
https://doi.org/10.1038/s41467-022-29694-7
要旨-2
Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that coleoid cephalopod genomes have been extensively restructured compared to other animals, leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identify a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understanding cephalopod innovations.
こちらはEuprymna scolopesについて，染色体レベルのアセンブリとATAC-seqによるオープンクロマチン領域の解析を行った論文．頭足類に特異的に見られるmicrosyntenyについて、転写の制御と三次元的な構造との関連や，神経系や体内器官における発現動態なども調べられている．
リファレンス-3
A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution.
Gavriouchkina, D., Tan, Y., Künzli-Ziadi, F., Hasegawa, Y., Piovani, L., Zhang, L., ... & Rokhsar, D. S. (2022). bioRxiv, 2022-05.
https://doi.org/10.1101/2022.05.26.490366
要旨-3
Although the camera-type eyes of cephalopods and vertebrates are a canonical example of convergent morphological evolution, the cellular and molecular mechanisms underlying this convergence remain obscure. We used genomics and single cell transcriptomics to study these mechanisms in the visual system of the bobtail squid Euprymna berryi, an emerging cephalopod model. Analysis of 98,537 cellular transcriptomes from the squid visual and nervous system identified dozens of cell types that cannot be placed in simple correspondence with those of vertebrate or fly visual systems, as proposed by Ramón y Cajal and J.Z. Young. Instead, we find an unexpected diversity of neural types, dominated by dopamine, and previously uncharacterized glial cells. Surprisingly, we observe changes in cell populations and neurotransmitter usage during maturation and growth of the visual systems from hatchling to adult. Together these genomic and cellular findings shed new light on the parallel evolution of visual system complexity in cephalopods and vertebrates.
Euprymna berryiの眼について，single-cell transcriptomeを行い，cell type の構成について脊椎動物や節足動物 (ショウジョウバエ) との比較を行った論文．リファレンスのため，Euprymna berryi自体のゲノムアセンブリも行っている．cell type レベルでは必ずしもdeep homology が見られるわけでも無いというのは興味深い．分子メカニズムレベルで異なるものが収斂して似たような機能・形態を示しているということか．また，発生に興味がある身としては，孵化個体と成長した幼体でoptic lobeの形態とともにcell typeも明らかに変化しているというのがとても面白い．細胞レベルで再構成されている様子を発現遺伝子のレベルから解明できるのは素晴らしいな．そこからまた形態の描写まで落とし込めると良いのだろう．
ゲノム関連ではないが，上の論文でも扱われているように，モデル頭足類として整備されつつあるEuprymna berryiとEuprymna morseiというミミイカ属の2種の飼育系確立についての論文も出ている．
リファレンス-4
Lifecycle, culture, and maintenance of the emerging cephalopod models Euprymna berryi and Euprymna morsei.
Jolly, J., Hasegawa, Y., Sugimoto, C., Zhang, L., Kawaura, R., Sanchez, G., ... & Rokhsar, D. (2022). Frontiers in Marine Science, 9.
https://doi.org/10.3389/fmars.2022.1039775
