High-coverage sequencing and annotated assemblies of the budgerigar genome.
High-coverage sequencing and annotated assemblies of the budgerigar genome.
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DOI：
10.1186/2047-217x-3-11
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发表时间：
2014
期刊：
影响因子：
9.2
通讯作者：
Jarvis ED
中科院分区：
文献类型：
--
作者：
Ganapathy G;Howard JT;Ward JM;Li J;Li B;Li Y;Xiong Y;Zhang Y;Zhou S;Schwartz DC;Schatz M;Aboukhalil R;Fedrigo O;Bukovnik L;Wang T;Wray G;Rasolonjatovo I;Winer R;Knight JR;Koren S;Warren WC;Zhang G;Phillippy AM;Jarvis ED
鹦鹉是一种行为先进的脊椎动物，相对于其他学习声音的鸟类，它具有先进的声音学习能力。他们可以模仿人类的语言，使他们的身体动作与有节奏的节拍同步，并理解声音所指意义的复杂概念。然而，人们对这些特征的遗传学知之甚少。阐明遗传基础需要全基因组测序和鹦鹉基因组的强大组装。我们提出了一个基因组资源的虎皮鹦鹉，澳大利亚鹦鹉（Melopsittacus undulatus）-最广泛研究的鹦鹉物种在神经科学和行为。我们提供了基因组序列数据，其中包括来自多种测序技术的超过300×原始读取覆盖率和来自单个雄性动物的染色体光学图谱。读取和光学图谱被用来创建三个杂交组件，代表了迄今为止鸟类的一些最大的基因组支架;其中两个基于与非冗余人类、斑胸草雀和鸡蛋白质的参考集以及虎皮鹦鹉转录组序列组件的相似性进行了注释。该项目的序列读取部分生成并用于装配子2竞争和利用PacBio单分子测序的千兆级脊椎动物基因组的首次从头组装。在几个质量指标上，这些虎皮鹦鹉组装体与从传统桑格测序读数构建的鸡和斑胸草雀基因组组装体相当或更好，并且足以分析难以测序和组装的区域，包括尚未在先前鸟类基因组中组装的区域，以及在发声学习脑区域中差异调节的基因的启动子区域。这项工作为基因组技术的发展和研究复杂行为特征的基因组学提供了有价值的数据和材料。
Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.