School of Natural Resources and the Environment, University of Arizona, 1311 East Fourth Street, Room 317, Tucson, AZ 85721, USA.
Mol Ecol Resour. 2012 Mar;12(2):191-6. doi: 10.1111/j.1755-0998.2011.03078.x. Epub 2011 Oct 4.
Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.
基于序列的物种鉴定依赖于在线数据库（如 GenBank）中可用的序列数据的范围和完整性。在从未知来源的样本中鉴定物种时，从样本中获得的部分 DNA 序列与数据库中的现有序列进行比对。当数据库中不存在与匹配物种相对应的序列时，与密切相关的序列的高分比对可能会对物种身份产生不可靠的结果。对于哺乳动物的物种鉴定，细胞色素 b（cyt b）基因已被确定为高度信息丰富；因此，非常需要大量来自 cyt b 基因的参考序列数据。为了在 GenBank 和其他此类公共可访问的在线数据库中增加大量哺乳动物物种的 cyt b 基因序列数据的可用性，我们确定了用于哺乳动物完整 cyt b 基因测序的引物对。使用该引物对，我们成功地从代表 10 个哺乳动物目 的 44 个哺乳动物物种中的 40 个物种中 PCR 扩增并测序了完整的 cyt b 基因。我们将 40 个完整的、正确注释的 cyt b 蛋白编码序列提交给 GenBank。据我们所知，这是第一个在广泛的哺乳动物物种中扩增完整 cyt b 基因的单一引物对。该引物对可用于添加新的 cyt b 基因序列并增强 GenBank 中代表的物种的数据可用性。新型和完整基因序列作为高质量参考数据的可用性可以提高基于序列的物种鉴定的可靠性。
