Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA.
US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, 538 Tower Rd, Ithaca, NY 14853, USA.
Gigascience. 2019 Apr 1;8(4). doi: 10.1093/gigascience/giz033.
The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.
The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate-glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.
A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
玉米穗蚜（Rhopalosiphum maidis Fitch）是玉米（Zea mays）上最具经济危害性的蚜虫害虫之一，玉米是世界上最重要的粮食作物之一。除了通过去除光合物直接造成损害外，R. maidis 还传播几种破坏性的玉米病毒，包括玉米黄矮病毒、大麦黄矮病毒、甘蔗花叶病毒和黄瓜花叶病毒。
使用太平洋生物科学公司（207 倍覆盖率）和 Illumina 公司（83 倍覆盖率）测序组合，组装了一个孤雌生殖的 R. maidis 克隆的基因组。689 个组装的连续序列，其 N50 大小为 9.0 兆碱基（Mb），杂合度低，使用 Phase Genomics Hi-C 相互作用图谱进行聚类。与 R. maidis 常见的 2n=8 核型一致，大多数连续序列（473 个跨越 321 Mb）成功定向到 4 个支架中。基因组组装捕获了核心真核基因全长的 95.8%，表明其高度完整。重复序列占组装的 21.2%，总共预测了 17629 个蛋白质编码基因，这些基因是通过从头预测和基于同源性的基因预测以及使用 Pacific Biosciences 和 Illumina 生成的转录组序列的综合证据预测的。对可能水平转移基因的分析鉴定了来自细菌的 2 个、来自真菌的 7 个、来自原生动物的 2 个和来自藻类的 9 个。在基因组序列中鉴定了重复元件、转座子和编码可能解毒酶（细胞色素 P450s、谷胱甘肽 S-转移酶、羧酸酯酶、尿苷二磷酸-葡萄糖基转移酶和 ABC 转运蛋白）的基因。除了 Buchnera aphidicola（642929 个碱基对，602 个基因），在 R. maidis 中没有发现其他内共生细菌。
组装了高质量的 R. maidis 染色体水平基因组。该基因组序列将使进一步研究生态相互作用、病毒传播、抗药性和 R. maidis 生物学的其他方面成为可能。它还为其他蚜虫物种的比较研究提供了有价值的资源。
