The challenge of Coccidae (Hemiptera: Coccoidea) mitochondrial genomes: The case of Saissetia coffeae with novel truncated tRNAs and gene rearrangements
The challenge of Coccidae (Hemiptera: Coccoidea) mitochondrial genomes: The case of Saissetia coffeae with novel truncated tRNAs and gene rearrangements
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球虫科（半翅目：球虫总科）线粒体基因组的挑战：具有新型截短 tRNA 和基因重排的咖啡塞塞蒂亚案例
DOI：
10.1016/j.ijbiomac.2020.04.257
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发表时间：
2020-09-01
影响因子：
8.2
通讯作者：
Deng, Jun
中科院分区：
文献类型：
--
作者：
Lu, Congcong;Huang, Xiaolei;Deng, Jun
目前关于介壳虫完整线粒体基因组（线粒体基因组）的报道较少，有人指出其线粒体基因组复杂而新颖的结构可能导致测序、组装和注释的困难。转移RNA（tRNA）通常具有典型的三叶草二级结构，而截短的tRNA在昆虫有丝分裂基因组中很少发现。在这里，我们报告了通过下一代测序（NGS）方法测序的完整的咖啡Saissetia coffeae线粒体基因组（15,389 bp），具有高A+T含量（84.7%）。对有丝分裂基因组中的基因进行了注释，使用 MITOS 未发现 9 个 tRNA。大多数检测到的 tRNA 均被显着截短，不含二氢尿苷 (DHU) 臂或 T.C (T) 臂。此外，根据我们研究中描述的球虫科 tRNA 注释工作流程，检索了 9 个包含错配碱基对的“丢失”tRNA。咖啡Saissetia coffeae 线粒体基因组中的基因排列与其他半翅目昆虫显着不同。此外，基于线粒体基因的贝叶斯树和最大似然树显示了Saissetia谱系的长分支，表明Saissetia谱系中存在显着的非同义替换或高进化率。我们为球虫科线粒体基因组的组装和注释提供了参考线粒体基因组，并为介壳虫的进化提供了见解。 (c) 2020 Elsevier B.V. 保留所有权利。
There have been fewreports of completemitochondrial genomes (mitogenomes) of scale insects, and it has been indicated that complex and novel structures in theirmitogenomes may lead to difficulties in sequencing, assembly and annotation. Transfer RNAs (tRNAs) usually possess typical cloverleaf secondary structures, and truncated tRNAs are rarely found in insect mitogenomes. Here, we report a complete Saissetia coffeae mitogenome (15,389 bp) with high A+T content (84.7%) sequenced by next-generation sequencing (NGS) methods. Genes in the mitogenome were annotated, and nine tRNAs were not found using MITOS. Most of the detected tRNAs were significantly truncated without the dihydrouridine (DHU) arm or the T.C (T) arm. In addition, the 9 "lost" tRNAs containing mismatched base pairs were retrieved based on the tRNA annotation workflow for Coccidae described in our study. The gene arrangement in the Saissetia coffeae mitogenomewas significantly different from that in other hemipteran insects. Additionally, Bayesian and maximum likelihood trees based on the mitochondrial genes showed a long branch of the Saissetia lineage, indicating significant nonsynonymous substitutions or high evolutionary rates in the Saissetia lineage. We provide a reference mitogenome for the assembly and annotation of the Coccidae mitogenome and offer insights into the evolution of scale insects. (c) 2020 Elsevier B.V. All rights reserved.