Additional file 1: of Gene annotation errors are common in the mammalian mitochondrial genomes database

Table S1. Analysis of gene arrangements of 304 mammalian mitochondrial genome. Gene arrangements of the mammalian species compared in this analysis as annotated at NCBI with Reference IDs shown for each. The numeral in parentheses indicates the number of species belonging to each group. Each gene is assigned a number 1–37 at the top of the Table which is then used to describe the annotated gene arrangement for each species. Each gene is transcribed left-to-right as shown except for those with a minus (−) symbol to indicate opposite orientation. The arrangement shared by all three monotreme and human mitochondrial genomes has long been inferred to be the ancestral condition for mammals. Highlighting indicates all deviations from that ancestral arrangement according to the NCBI sequence records, with green being confirmed by this work, red being errors of gene arrangement according to our analysis, brown being errors of gene boundary annotation according to our observation, orange being a failure to annotate a gene that we determined to be present, and gray being a gene missing wholly or in large part because the sequence is not present in the file. trnY for Aotus nancymaae, colored red here, is also in error for gene boundary errors. 1Extinct species. (XLSX 62 kb)

表S1：304种哺乳动物线粒体基因组基因排列分析。本分析中比较的各哺乳动物物种的基因排列模式，均基于美国国家生物技术信息中心（National Center for Biotechnology Information，NCBI）的注释，且为每个物种标注了参考编号。括号内的数字代表对应类群所包含的物种数量。表格顶部将每个基因编号为1至37，以此描述各物种的注释基因排列情况。除带有减号（−）的基因表示转录方向相反外，其余基因均按图示从左至右转录。此前学界普遍认为，所有单孔目动物与人类线粒体基因组共有的基因排列模式，即为哺乳动物线粒体基因组的祖先状态。高亮标注部分代表根据NCBI序列记录与该祖先排列模式的所有偏差，各类偏差的含义如下：绿色为本研究证实的偏差；红色为本研究分析确认的基因排列错误；棕色为本研究观察到的基因边界注释错误；橙色为本研究确认存在但未被注释的基因；灰色为因序列文件缺失而整体或大部分缺失的基因。夜猴（Aotus nancymaae）的trnY基因此处标注为红色，同时也存在基因边界注释错误。¹ 已灭绝物种。（XLSX 62 kb）