Phylogenomic Studies on the Evolution of Morphological Complexity

形态复杂性演化的系统基因组学研究

• 批准号: 8565527
• 负责人: Andreas Baxevanis
• 金额: $ 42.28万
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8565527
• 关键词: Animals; Biogenesis; Bioinformatics; Bioluminescence; Calcium; Case Study; Cells; Classification; Cnidaria; Collection; Communities; Ctenophora; Data; Data Set; Deltastab; Deposition; Development; Developmental Biology; Disease Outbreaks; Event; Evolution; Explosion; Eye; Family; Family member; Follistatin; Future; Genbank; Gene Duplication; Gene Expression; Gene Expression Regulation; Gene Family; Generations; Genes; Genome; Genomics; Goals; Hawaii; Health; Homeobox; Homologous Gene; Human; Iowa; LIM Domain; Length; Life Style; Ligands; Light; Link; Luminescent Proteins; Marines; Mediating; MicroRNAs; Mitochondria; Mitochondrial DNA; Mnemiopsis; Molecular; Nuclear; Nuclear Proteins; Opsin; Oral; Organism; Paper; Pathway interactions; Pattern Formation; Phylogenetic Analysis; Phylogeny; Play; Porifera; Positioning Attribute; Preparation; Production; Protein Family; Proteins; Publications; RNA Sequences; Relative (related person); Reporting; Research; Resources; Ribosomal Proteins; Ribosomal RNA; Role; Signal Transduction; Specific qualifier value; Stimulus; Structure; System; TGF Beta Signaling Pathway; Taxon; Techniques; Time; Transfer RNA; Trees; Universities; Vision; Work; base; cell type; chordin; comparative genomics; document outlines; extracellular; functional genomics; genome sequencing; homeodomain; human disease; innovation; mitochondrial genome; novel; programs; protein function; receptor; stem; transcription factor

This research program focuses on the use of phylogenetic and comparative genomic techniques to better-understand the evolution of homeodomain transcription factors and their role in pattern formation and cell fate determination during metazoan development. A variety of bioinformatic approaches are used to understand the evolution and function of these proteins and their ultimate role in human disease. Homeobox (or Hox) genes are organized in conserved genomic clusters across a range of phylogenetic taxa. Over evolutionary time, the functional diversification of these Hox genes has contributed to the diversification of animal body plans. Building upon our prior work on the origin and early evolution of these Hox genes, our focus has turned to analyzing the genomes of early-branching metazoan phyla to better-understand the relationship between genomic complexity and morphological complexity, as well as the molecular basis for the evolution of novel cell types. Until recently, only three of the four non-bilaterian metazoan lineages (Porifera, Placozoa, and Cnidaria) had at least one species whose genome had been sequenced. Ctenophora (the comb jellies) remained as the last non-bilaterian animal phylum without a sequenced genome, and its phylogenetic position remained uncertain. With the goal of understanding the molecular innovations that drove the outbreak of diversity and increasing complexity in the early evolution of animals, we sequenced, assembled, annotated, and performed a preliminary analysis of the 150-megabase genome of the ctenophore, Mnemiopsis leidyi. Our sequence assembly was deposited into GenBank earlier this year, and the paper describing this genome will be submitted for publication shortly (Ryan et al., in preparation). Thematically, our sequencing project (and subsequent analyses) aligns quite well with a significant number of themes elucidated in NHGRI's most recent document outlining a vision for the future of genomic research -- most importantly, the need to probe the interface between genomics and developmental biology, as well as to conduct comparative, genomics-based research with an evolutionary point-of-view. The availability of these sequence data has already begun to benefit multiple scientific communities (i.e., marine, evolutionary, and developmental biologists) and has enabled us to answer some important questions regarding phylogenetic diversity and the evolution of proteins that play a fundamental role in metazoan development. For example, during this reporting period, we were able to identify and characterize all known LIM domain-containing proteins in six metazoans and three non-metazoans (Koch et al., 2012). Using this data set, phylogenetic analyses were performed, yielding a number of novel non-LIM domains and motifs in each of these proteins. This allowed us to formalize a classification system for the LIM proteins, determine the relative timing for class- and family-origin events, and identify lineage-specific loss events. This study determined that six of the 14 LIM classes originated in the metazoan stem lineage, and the observed expansion of the LIM superclass at the base of the Metazoa allowed for the increase in complexity required for the transition from a unicellular to multicellular lifestyle. Put otherwise, these evolutionary events recount a critical step in the emergence of multicellularity in animal species. We have also focused on the vital role that microRNAs play in the regulation of gene expression. Using short RNA sequencing data and the assembled Mnemiopsis genome, we were able to show that this species appears to lack any recognizable microRNAs, as well as the nuclear proteins Drosha and Pasha, which are critical to canonical microRNA biogenesis. (Maxwell et al., submitted). This finding represents the first reported case of a metazoan lacking a Drosha protein. Since our recent phylogenomic analyses suggest that Mnemiopsis may be the earliest branching metazoan lineage, then these findings provide support for the origins of canonical microRNA biogenesis and microRNA-mediated gene regulation post-dating the last common metazoan ancestor. Alternatively, canonical microRNA functionality may have been lost independently in early lineages, suggesting that microRNA functionality was not critical until much later in metazoan evolution. In either case, these data shed light on a point in evolutionary time that may have predated the need for additional plasticity in developmental signaling networks. Our recent completion of the sequencing of Mnemiopsis has also provided us with the opportunity to examine the genome of an organism that uses calcium-activated photoproteins for bioluminescence. We found two genomic clusters containing a total of at least 10 full-length photoprotein genes that likely arose due to multiple gene duplication events, providing the basis for the first metazoan phylogeny for the photoprotein gene family; the phylogeny indicates that this gene family arose at the base of the Metazoa (Schnitzler et al., submitted). We also were able to demonstrate co-localized expression of photoprotein genes and two putative opsin genes in developing Mnemiopsis photocytes, showing for the first time that these cells have the capacity to both sense and respond to stimuli. This is the first reported instance of photoreception and light production co-occurring and being functionally linked in the same cell of a single organism. These findings may shed new light on the evolution of the eye, especially during the Cambrian explosion. With our collaborators at Iowa State University, an analysis of the mitochondrial (mt-) genome of Mnemiopsis was performed (Pett et al., 2011). At just over 10 kb, the mtDNA of Mnemiopsis is the smallest animal mtDNA reported to date, and it is also among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. It appears that atp6 has been relocated to the nuclear genome and has acquired a mitochondrial targeting presequence. Encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear-encoded mt-ribosomal proteins have undergone expansions, which may compensate for the reductions in mt-rRNA. With our collaborators at the University of Hawaii, we were able to identify a near-complete TGF-beta signaling pathway composed of nine ligands, four receptors, and five Smads, revealing that the core components are present in all metazoans studied to date (Pang et al., 2011). Notably absent are extracellular diffusible antagonists, including Chordin, Follistatin, Noggin, and CAN family members. We examined the expression of these genes during ctenophore development and found expression of ligands to be differentially expressed along all three body axes (i.e., oral-aboral, tentacular, and sagittal). While we do not believe this pathway is necessarily specifying these axes since they are expressed after the axes are already specified, we do believe they are involved with transducing earlier signals. These findings indicate that the TGF-beta signaling pathway was present and most likely active early in metazoan evolution. With few components present in extant non-metazoans, it is highly probable that the emergence of this pathway was a key innovation in the transition to multicellularity in the metazoan ancestor. As an outgrowth of our studies on the homeodomain class of proteins, we have developed and continue to maintain the Homeodomain Resource, a curated collection of sequence, structure, interaction, genomic, and functional information on the homeodomain family (Moreland et al., 2009). The Resource is organized in a compact form and provides user-fr

该研究项目的重点是利用系统发育和比较基因组技术来更好地了解同源域转录因子的进化及其在后生动物发育过程中模式形成和细胞命运决定中的作用。多种生物信息学方法用于了解这些蛋白质的进化和功能及其在人类疾病中的最终作用。 同源盒（或 Hox）基因在一系列系统发育类群中组织在保守的基因组簇中。随着进化时间的推移，这些 Hox 基因的功能多样化促进了动物身体结构的多样化。基于我们之前对这些 Hox 基因的起源和早期进化的研究，我们的重点转向分析早期分支后生动物门的基因组，以更好地理解基因组复杂性和形态复杂性之间的关系，以及新型细胞类型进化的分子基础。 直到最近，四种非对称动物后生动物谱系（多孔动物门、扁动物门和刺胞动物门）中只有三个至少有一个物种的基因组已被测序。栉水母（栉水母）仍然是最后一个没有基因组测序的非对称动物门，其系统发育位置仍然不确定。为了了解动物早期进化中推动多样性爆发和复杂性不断增加的分子创新，我们对栉水母 Mnemiopsis leidyi 的 150 兆碱基基因组进行了测序、组装、注释和初步分析。我们的序列组装已于今年早些时候存入 GenBank，描述该基因组的论文将很快提交出版（Ryan 等人，正在准备中）。从主题上看，我们的测序项目（以及随后的分析）与 NHGRI 最新文件中阐明的大量主题非常吻合，该文件概述了基因组研究的未来愿景——最重要的是，需要探索基因组学和发育生物学之间的接口，以及从进化的角度进行基于基因组学的比较研究。 这些序列数据的可用性已经开始使多个科学界（即海洋、进化和发育生物学家）受益，并使我们能够回答一些有关系统发育多样性和在后生动物发育中发挥基本作用的蛋白质进化的重要问题。例如，在本报告期内，我们能够识别和表征六种后生动物和三种非后生动物中所有已知的含有 LIM 结构域的蛋白质（Koch 等，2012）。使用该数据集进行系统发育分析，在每种蛋白质中产生了许多新颖的非 LIM 结构域和基序。这使我们能够正式确定 LIM 蛋白的分类系统，确定类和科起源事件的相对时间，并识别谱系特异性丢失事件。这项研究确定 14 个 LIM 类中的 6 个起源于后生动物干谱系，并且观察到 LIM 超类在后生动物基部的扩张使得从单细胞生活方式过渡到多细胞生活方式所需的复杂性增加。换句话说，这些进化事件讲述了动物物种多细胞性出现的关键一步。 我们还关注 microRNA 在基因表达调控中发挥的重要作用。使用短 RNA 测序数据和组装的 Mnemiopsis 基因组，我们能够证明该物种似乎缺乏任何可识别的 microRNA，以及核蛋白 Drosha 和 Pasha，这对典型的 microRNA 生物发生至关重要。 （Maxwell 等人提交）。这一发现代表了第一个报告的后生动物缺乏 Drosha 蛋白的病例。由于我们最近的系统发育分析表明 Mnemiopsis 可能是最早分支的后生动物谱系，因此这些发现为经典的 microRNA 生物发生和 microRNA 介导的基因调控的起源提供了支持，这些基因调控可追溯到最后一个常见的后生动物祖先。或者，典型的 microRNA 功能可能在早期谱系中独立丢失，这表明 microRNA 功能直到很晚的后生动物进化中才变得至关重要。无论哪种情况，这些数据都揭示了进化时间中的一个点，该点可能早于发育信号网络中额外可塑性的需要。 我们最近完成的 Mnemiopsis 测序也为我们提供了检查使用钙激活光蛋白进行生物发光的生物体基因组的机会。我们发现了两个基因组簇，总共包含至少 10 个全长发光蛋白基因，这些基因可能是由于多个基因重复事件而产生的，为发光蛋白基因家族的第一个后生动物系统发育提供了基础；系统发育表明该基因家族起源于后生动物的基础（Schnitzler 等人提交）。我们还能够证明发光蛋白基因和两个假定的视蛋白基因在发育中的 Mnemiopsis 光细胞中的共定位表达，首次表明这些细胞具有感知和响应刺激的能力。这是第一个报道的光接收和光产生在单个生物体的同一细胞中同时发生并在功能上联系在一起的实例。这些发现可能为眼睛的进化提供新的线索，特别是在寒武纪大爆发期间。 我们与爱荷华州立大学的合作者一起对 Mnemiopsis 的线粒体 (mt-) 基因组进行了分析 (Pett et al., 2011)。 Mnemiopsis 的 mtDNA 仅超过 10 kb，是迄今为止报道的最小的动物 mtDNA，也是衍生最多的动物 mtDNA 之一。它丢失了至少25个基因，包括atp6和所有tRNA基因。看来 atp6 已重新定位到核基因组并获得了线粒体靶向前序列。编码的 rRNA 分子与其他生物体中的同源物几乎没有相似性，并且二级结构大大减少。与此同时，核编码的 mt-核糖体蛋白发生了扩增，这可能补偿 mt-rRNA 的减少。 与夏威夷大学的合作者一起，我们能够识别出由九个配体、四个受体和五个 Smad 组成的近乎完整的 TGF-β 信号通路，揭示了迄今为止研究的所有后生动物中都存在核心成分（Pang 等，2011）。值得注意的是，细胞外扩散拮抗剂不存在，包括 Chordin、Follistatin、Noggin 和 CAN 家族成员。我们检查了这些基因在栉水母发育过程中的表达，发现配体的表达沿着所有三个身体轴（即口口、触手和矢状）差异表达。虽然我们不认为该通路一定指定这些轴，因为它们是在轴已经指定后表达的，但我们确实相信它们涉及转导早期信号。这些发现表明TGF-β信号通路在后生动物进化的早期就存在并且很可能活跃。由于现存的非后生动物中存在很少的成分，因此该途径的出现很可能是后生动物祖先向多细胞性过渡的关键创新。 作为我们对同源域类蛋白质研究的成果，我们开发并继续维护同源域资源，这是同源域家族的序列、结构、相互作用、基因组和功能信息的精选集合（Moreland 等，2009）。该资源以紧凑的形式组织，并为用户提供