海洋國家實驗室在扇貝基因組精細圖譜繪製和動物宏觀進化領域取得重要進展

本文轉載自微信公眾號海洋國家實驗室

2017年4月3日，青島海洋科學與技術國家實驗室（以下簡稱「海洋國家實驗室」）、中國海洋大學包振民教授領銜的國際研究團隊首次完成了扇貝基因組精細圖譜繪製，並在動物宏觀進化研究領域取得重要進展。在探究原始動物祖先（Urbilateria）染色體核型進化、軀體結構多樣性產生、眼睛起源及其調控機制等方面取得多項新發現和新認識，為理解動物早期演化機制提供關鍵線索。

來源 青島海洋科學與技術國家實驗室

該研究成果發表在國際生態與進化領域期刊Nature Ecology & Evolution上（論文信息見文末）。海洋國家實驗室海洋漁業科學與食物產出過程功能實驗室、中國海洋大學包振民教授和海洋國家實驗室海洋生物學與生物技術功能實驗室、中國海洋大學王師教授分別為該文的通訊作者和第一作者。該成果是在海洋國家實驗室鰲山科技創新計劃項目支持下取得的優秀代表成果，同時得到了海洋國家實驗室鰲山人才「優秀青年學者」項目等資助。

現今地球上，動物界99%的物種隸屬雙側對稱動物（bilaterian），寒武世生命大爆發，雙側對稱動物大量出現，進而演化形成了我們今天地球上動物界主要類群的基本格局。進化學家推測這些雙側對稱動物可能起源於一個古老的共同祖先（Urbilateria），但由於早期動物化石記錄匱乏，長期以來人們對雙側對稱動物的起源和進化機制存有較多爭議。

通過對現存古老動物類群基因組比較分析，以重構並推斷雙側對稱動物祖先的基因組特徵，被認為是解決這些爭議的關鍵途徑。目前對動物基因組進化的認知主要來源於兩大動物類群（後口動物和蛻皮動物），而對於最為古老的第三大類群冠輪動物，仍所知甚少。解析原始冠輪動物類群（如起源於距今5億年前早寒武世的貝類）的基因組特徵，可為理解動物早期起源和進化機制提供關鍵線索。

研究發現

包振民教授團隊作為國際扇貝基因組計劃的發起者，領導完成了首張高質量扇貝全基因組圖譜繪製。通過對扇貝基因組深度解析，揭示扇貝呈現眾多原始動物祖先基因組特徵，近乎完美地保存了動物祖先的染色體核型、保留數目最多的古老基因家族、具有最完整的 Hox、ParaHox、NK 基因簇的基因組序列等，為迄今已發現的最古老的雙側對稱動物基因組，為研究雙側對稱動物早期起源進化提供了難得的基因組模型。

扇貝(P. yessoensis) 近乎完美地保留了雙側對稱動物祖先的染色體核型

進一步研究發現扇貝控制軀體模式（body plan）發育的Hox基因簇呈「分段共線性」表達模式，與目前普遍認為 Hox 基因簇遵循「完全時空共線性」表達模式不同。深入研究揭示「分段共線性」表達模式在低等動物普遍存在，是一種獨特、古老的軀體模式決定機制，為理解寒武世動物軀體模式多樣化的起源和進化機制提供了新視野。

Hox基因簇「分段共線性(STC)」調控新模式及其可能的起源和演化途徑

扇貝具有數十至上百的鏡眼，研究還發現扇貝眼睛擁有不同尋常的多套光傳導通路系統，其眼睛發生由 pax2/5/8 基因而非 pax6 基因主導，對目前國際主流的眼睛單源起源假說（pax6控制）提出了挑戰，為動物體側眼獨立於頭眼起源進化的新假說提供關鍵證據。上述重要發現將貝類在動物進化研究領域提升到一個新地位，拓展和加深了當前學術界對雙側對稱動物的早期起源和演化機制的認識。

扇貝眼睛擁有多套光傳導通路系統

題目Scallop genome provides insights into evolution of bilaterian karyotype and development

作者Shi Wang, Jinbo Zhang, Wenqian Jiao, et al

在線發表日期03 April 2017

摘要Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

The nature of Urbilateria, the last common ancestor of all bilaterians, is enigmatic due to the lack of a plausible candidate in the fossil records 1 . The earliest unambiguous fossil of a bilaterian, Kimberella, shows remarkable resemblance to a mollusc, albeit its relationship with Urbilateria remains uncertain 2,3 . In the absence of definitive fossil records, genomic reconstruction by comparing extant bilaterian genomes becomes essential to our understanding of early bilaterian ancestors and their subsequent evolution 4,5 . However, reconstructing the genome of the bilaterian ancestor is challenging due to the paucity of high-order genome assemblies from ancient and/or slow-evolving lineages. Early genome sequencing efforts have mostly focused on two of the three major bilaterian groups, that is, protostome ecdysozoans and deuterostomes. Limited sequencing in the third group of protostome lophotrochozoans, a large superclade that includes molluscs, annelids and brachiopods, has revealed that their genomes are less derived from the ancestral bilaterian state than those of many ecdysozoans 5 . Unfortunately, none of these less-derived lophotrochozoan genomes were assembled to a degree that permits chromosome-level genome comparison.

Mollusca is the most speciose phylum of Lophotrochozoa and among the first bilaterians to appear in fossil records 6 . Many molluscan lineages including bivalves showed little change in shell morphology and life style over several hundred million years, and yet extant molluscs are abundant and thriving in diverse marine, freshwater and terrestrial environments, providing key ecological services and significant economic benefits to humans. Molluscs are highly diverse in form, making them excellent subjects to study body plan evolution and in particular its patterning by Hox genes 7 . Molluscs also have the greatest diversity in eye morphology, ranging from simple cupped to chambered or compound eyes, as well as in the number and placement of their eyes 8 , providing good subjects to study the origin and evolution of the eye, or Darwin』s 『organ of extreme perfection』. Despite the great evolutionary and biological significance of molluscs, our sampling of their genomes remains limited to a few species 5,9,10,11 and without high-order assemblies.

Here we report a high-quality, chromosome-anchored reference genome of the scallop Patinopecten yessoensis (Jay, 1857), a bivalve mollusc from the large Pectinidae family that contains ~270 living species and thousands of fossil species (dating back to ~320–340 million years ago, Ma 12 ). Scallops are widely distributed in world oceans. They are mostly free-living and have multiple eyes scattering along the mantle edge. Many scallops are important fishery and aquaculture species. P. yessoensis is a large scallop living on cold and stable ocean bottoms of the northwestern Pacific. It has a conserved 19-chromosome karyotype that is common to diverse bivalves and may represent the ancient karyotype of bivalves 13 . Analysis of the scallop genome and extensive transcriptomes reveals outstanding preservation of ancestral bilaterian linkage groups, an intact Hox gene cluster under new expression control and diverse phototransduction cascades with a potentially ancient Pax2/5/8-dependent pathway for noncephalic eye formation, providing insights into the evolution of genome organization and developmental control during the emergence of bilaterians.

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