Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France.
Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico.
G3 (Bethesda). 2023 Dec 6;13(12). doi: 10.1093/g3journal/jkad239.
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
残余物种，如腔棘鱼、银杏、楔齿蜥，是曾经更为生态和分类多样化的谱系的残余。这就提出了为什么它们目前物种较少、生态受限，而且往往容易灭绝的问题。估计杂合度水平和种群历史可以指导我们理解残余物种的进化历史和保护状况。然而，与脊椎动物相比，很少有研究关注残余无脊椎动物。我们对处于濒危状态的珍奇凤蝶（鳞翅目：凤蝶科）进行了基因组测序，它是所有燕尾蝶的姐妹种，也是所有现存蝴蝶中最古老的谱系。从一个干燥的标本中，我们生成了长读和短读数据，并组装了珍奇凤蝶 4.06 亿碱基对的基因组。与其他燕尾蝶相比，我们发现其杂合度相当高（0.58%），这与它的濒危和残余状况形成了对比。考虑到重组与突变的高比值，种群动态分析表明，在过去的 100 万年中，有效种群数量急剧下降。此外，珍奇凤蝶的基因组被用于研究凤蝶科的基因组大小变异。基因组大小主要由转座元件的活性来解释，这表明大基因组似乎是燕尾蝶的一个衍生特征，因为转座元件的活性是最近的，并且涉及到不同的转座元件类别。第一个珍奇凤蝶基因组为保护旗舰和残余昆虫物种以及理解燕尾蝶的基因组进化提供了资源。
