Meiring Christina, Eygelaar Monique, Fourie Josephus, Labuschagne Michel
Clinglobal, B03/04, The Tamarin Commercial Hub, Tamarin, 90903, Mauritius.
Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa.
BMC Genomics. 2025 Jul 1;26(1):591. doi: 10.1186/s12864-025-11733-4.
The assembly of large and complex genomes can be costly since it typically requires the utilization of multiple sequencing technologies and access to high-performance computing, while creating a dependency on external service providers. The aim of this study was to independently generate draft genomes for the cattle ticks Rhipicephalus microplus and R. appendiculatus using Oxford Nanopore sequencing technology.
Exclusively, Oxford Nanopore sequence data were assembled with Shasta and finalized on the Amazon Web Services cloud platform, capitalizing on the availability of up to 90% discounted Spot instances. The assembled and polished R. microplus and R. appendiculatus genomes from our study were comparable to published tick genomes where multiple sequencing technologies and costly bioinformatic resources were utilized that are not readily accessible to low-resource environments. We predicted 52,412 genes for R. appendiculatus, with 31,747 of them being functionally annotated. The R. microplus annotation consisted of 60,935 predicted genes, with 32,263 being functionally annotated in the final file. The sequence data were also used to assemble and annotate genetically distinct Coxiella-like endosymbiont genomes for each tick species. The results indicated that each of the endosymbionts exhibited genome reductions. The Nanopore Q20 + library kit and flow cell were used to sequence the > 80% AT-rich mitochondrial DNA of both tick species. The sequencing generated accurate mitochondrial genomes, encountering imperfect base calling only in homopolymer regions exceeding 10 bases.
This study presents an alternative approach for smaller laboratories with limited budgets to enter the field and participate in genomics without capital intensive investments, allowing for capacity building in a field normally exclusively accessible through collaboration and large funding opportunities.
大型复杂基因组的组装成本高昂，因为通常需要使用多种测序技术并借助高性能计算，同时还依赖外部服务提供商。本研究的目的是使用牛津纳米孔测序技术独立生成微小扇头蜱和安氏扇头蜱的基因组草图。
仅使用牛津纳米孔序列数据，通过Shasta进行组装，并在亚马逊网络服务云平台上完成，利用了高达90%折扣的现货实例。我们研究中组装和优化后的微小扇头蜱和安氏扇头蜱基因组，与已发表的蜱类基因组相当，而已发表的基因组使用了多种测序技术和昂贵的生物信息学资源，低资源环境难以获取。我们预测安氏扇头蜱有52,412个基因，其中31,747个具有功能注释。微小扇头蜱的注释包括60,935个预测基因，最终文件中有32,263个具有功能注释。序列数据还用于组装和注释每个蜱种的遗传上不同的类柯克斯体共生菌基因组。结果表明，每个共生菌都呈现出基因组缩减。使用纳米孔Q20 +文库试剂盒和流动槽对两种蜱类超过80%富含AT的线粒体DNA进行测序。测序生成了准确的线粒体基因组，仅在超过10个碱基的同聚物区域遇到碱基识别不完美的情况。
本研究为预算有限的较小实验室提供了一种替代方法，使其无需大量资本投资即可进入该领域并参与基因组学研究，从而在一个通常只能通过合作和大量资金机会才能进入的领域实现能力建设。
