Schuster Astrid, Lopez Jose V, Becking Leontine E, Kelly Michelle, Pomponi Shirley A, Wörheide Gert, Erpenbeck Dirk, Cárdenas Paco
Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA.
BMC Evol Biol. 2017 Mar 20;17(1):82. doi: 10.1186/s12862-017-0928-9.
Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns.
For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated.
This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.
线粒体内含子间断基因的编码区域，具有特征性的二级结构和剪接机制。在后生动物中，仅在海绵动物、刺胞动物、扁盘动物和一种环节动物物种中检测到线粒体内含子。在寻常海绵纲中，I 组和 II 组内含子存在于六个科中。基于细胞色素氧化酶亚基 1（cox1）基因内不同的插入位点和二级结构，已知四种类型的 I 组内含子和两种类型的 II 组内含子，它们最多可携带三个编码 LAGLIDADG 家族归巢内切核酸酶基因（HEG）（I 组）和/或逆转录酶（II 组）。然而，由于缺乏全面的数据集，关于海绵内含子的移动性、传播和起源知之甚少。我们分析了迄今为止关于海绵线粒体 I 组内含子的最大数据集：来自 11 个不同海绵属的 95 个标本，为 I 组内含子的进化提供了新的见解。
首次在硬皮海绵科的四个属（硬皮海绵属、微硬皮海绵属、针骨海绵属、硬壳海绵属）中检测到 I 组内含子。我们证明海绵中的 I 组内含子聚集在 cox1 最保守的区域。我们表明 cox1 中两个内含子同时出现在后生动物中是独特的，但在海绵中并不罕见。然而，这种组合总是将一个活跃的内含子与一个退化的内含子联系在一起。早期关于水平基因转移（HGT）的假设得到了证实，首次确凿地证明了垂直基因转移（VGT）和内含子的二次丢失。
本研究证实螺旋海绵亚纲（寻常海绵目）是海绵中的内含子热点。我们的分析证实，大多数海绵 I 组内含子可能起源于真菌。讨论了 DNA 条形码，并建议了替代引物的应用。
