Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus)
Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus)
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DOI：
10.1007/s00251-020-01197-z
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发表时间：
2021-02-05
期刊：
影响因子：
3.2
通讯作者：
Belov, Katherine
中科院分区：
文献类型：
--
作者：
Peel, Emma;Frankenberg, Stephen;Belov, Katherine
基因组测序技术的进步使得灭绝物种的基因组能够被测序。然而，考虑到这些基因组组装体的碎片性质，尚不清楚是否有可能全面注释高度可变和重复的基因，例如与免疫相关的基因。因此，免疫基因仅在少数已灭绝的基因组中进行了研究，主要是在人类谱系中。 2018 年，我们对袋狼 (Thylacinus cynocephalus) 的基因组进行了测序，袋狼是一种来自塔斯马尼亚的肉食性有袋动物，于 1936 年灭绝。在这里，我们试图描述袋狼的免疫系统特征，并确定其与现有基因组的最近亲塔斯马尼亚袋獾（Sarcophilus harrisii）以及其他有袋动物的相似性。鉴定了所有主要免疫基因家族的成员。然而，可变区无法表征，并且主要组织相容性复合物（MHC）等复杂家族高度碎片化并位于多个小支架上。因此，在基因水平上，我们无法重建大多数袋狼免疫基因的全长编码序列。尽管如此，我们还是鉴定出了编码功能上重要的受体和免疫效应分子的基因，这表明袋狼免疫系统的功能能力与其他哺乳动物相似。然而，大量已鉴定的部分免疫基因序列限制了我们重建袋狼免疫库的准确图像的能力。
Advances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylacine and determine similarity to its closest relative with a genome available, the Tasmanian devil (Sarcophilus harrisii), as well as other marsupials. Members from all major immune gene families were identified. However, variable regions could not be characterised, and complex families such as the major histocompatibility complex (MHC) were highly fragmented and located across multiple small scaffolds. As such, at a gene level we were unable to reconstruct full-length coding sequences for the majority of thylacine immune genes. Despite this, we identified genes encoding functionally important receptors and immune effector molecules, which suggests the functional capacity of the thylacine immune system was similar to other mammals. However, the high number of partial immune gene sequences identified limits our ability to reconstruct an accurate picture of the thylacine immune repertoire.