A chromosome-scale assembly of the major African malaria vector Anopheles funestus
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
复制标题
DOI：
10.1093/gigascience/giz063
复制
发表时间：
2019-06-01
期刊：
影响因子：
9.2
通讯作者：
Besansky, Nora J.
中科院分区：
文献类型：
--
作者：
Ghurye, Jay;Koren, Sergey;Besansky, Nora J.
背景：不死按蚊是非洲热带地区人类疟疾的3种最重要和最广泛的媒介之一。然而，缺乏高质量的参考基因组阻碍了这种重要蚊子的表型性状与其遗传基础的关联。结果：在这里，我们提出了一个新的高质量的A。使用240倍覆盖度的长读单分子测序进行重叠拼接，结合100倍覆盖度的短读Hi-C数据进行染色体支架构建，组装funestus参考基因组（AfunF 3）。组装的重叠群共有446 Mbp的序列，并且由于来自FUMOZ菌落的蚊子的测序池中存在的替代等位基因而含有大量重复。使用比对和覆盖深度信息，将这些重叠群去重复成211 Mbp的初级组装体，其更接近预期的250 Mbp的单倍体基因组大小。该初级组装体由1，053个重叠群组成，组成3个染色体规模的支架，N50重叠群大小为632 kbp，N50支架大小为93.811 Mbp，与当前参考组装体AfunF 1相比，连续性提高了100倍。结论：该高度连续和完全的A. funestus参考基因组组装将作为今后研究这一重要疾病载体的基因组变异和组织的改进基础。
Background: Anopheles funestus is one of the 3 most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito. Findings: Here we present a new high-quality A. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for contigging, combined with 100x coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1. Conclusion: This highly contiguous and complete A. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.