Richardson Mark F, Munyard Kylie, Croft Larry J, Allnutt Theodore R, Jackling Felicity, Alshanbari Fahad, Jevit Matthew, Wright Gus A, Cransberg Rhys, Tibary Ahmed, Perelman Polina, Appleton Belinda, Raudsepp Terje
Genomics Centre, Deakin University, Geelong, VIC, Australia.
Centre for Integrative Ecology, Deakin University, Geelong, VIC, Australia.
Front Genet. 2019 Jun 21;10:586. doi: 10.3389/fgene.2019.00586. eCollection 2019.
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome presents a significant improvement in completeness, contiguity and accuracy over and is an important tool for the advancement of genomics research in all New World camelids.
高质量的染色体定位参考基因组的发展是理解一个物种基因组结构的关键特征，对于发现具有生物学意义的性状的遗传蓝图至关重要。南美骆驼科动物在极端环境中为人类服务，是全球重要的纤维和伴侣动物。尽管如此，羊驼参考基因组仍远远落后于其他家养物种的参考基因组。在这里，我们使用与之前组装相同的雌性瓦卡亚羊驼的DNA，为羊驼基因组生成了一个染色体水平的改进参考组装。我们为该组装生成了190倍的Illumina短读长、8倍的PacBio长读长和60倍的Dovetail Chicago染色质相互作用支架数据，使用睾丸和皮肤RNAseq数据进行注释，并使用细胞遗传图谱数据进行染色体定位。新的组装在仅103个支架中包含了90%的羊驼基因组，并且76%的支架被定位到36对羊驼常染色体和X染色体上。该组装的初步注释预测了22462个编码基因和29337个异构体。对羊驼基因组选定区域的比较分析，如主要组织相容性复合体（MHC）、参与（MCS）的区域和高原适应候选基因，揭示了羊驼基因组的独特特征。与之前的版本相比，羊驼参考基因组在完整性、连续性和准确性方面有了显著提高，是推进所有新大陆骆驼科动物基因组学研究的重要工具。
