A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS) genes.

Due to their potential roles in pathogen defense, genes encoding nucleotide-binding site (NBS) domain have been particularly surveyed in many angiosperm genomes. Two typical classes were found: one is the TIR-NBS-LRR (TNL) class and the other is the CC-NBS-LRR (CNL) class. It is seldom known, however, what kind of NBS-encoding genes are mainly present in other plant groups, especially the most ancient groups of land plants, that is, bryophytes. To fill this gap of knowledge, in this study, we mainly focused on two bryophyte species: the moss Physcomitrella patens and the liverwort Marchantia polymorpha, to survey their NBS-encoding genes. Surprisingly, two novel classes of NBS-encoding genes were discovered. The first novel class is identified from the P. patens genome and a typical member of this class has a protein kinase (PK) domain at the N-terminus and a LRR domain at the C-terminus, forming a complete structure of PK-NBS-LRR (PNL), reminiscent of TNL and CNL classes in angiosperms. The second class is found from the liverwort genome and a typical member of this class possesses an α/β-hydrolase domain at the N-terminus and also a LRR domain at the C-terminus (Hydrolase-NBS-LRR, HNL). Analysis on intron positions and phases also confirmed the novelty of HNL and PNL classes, as reflected by their specific intron locations or phase characteristics. Phylogenetic analysis covering all four classes of NBS-encoding genes revealed a closer relationship among the HNL, PNL and TNL classes, suggesting the CNL class having a more divergent status from the others. The presence of specific introns highlights the chimerical structures of HNL, PNL and TNL genes, and implies their possible origin via exon-shuffling during the quick lineage separation processes of early land plants.

由于其在病原体防御中的潜在作用，编码核苷酸结合位点（NBS）结构域的基因在许多被子植物基因组中受到了特别的研究。发现了两种典型的类别：一种是TIR - NBS - LRR（TNL）类，另一种是CC - NBS - LRR（CNL）类。然而，对于其他植物类群，尤其是最古老的陆地植物类群，即苔藓植物中主要存在何种编码NBS的基因，却知之甚少。为了填补这一知识空白，在本研究中，我们主要关注两种苔藓植物：小立碗藓（Physcomitrella patens）和地钱（Marchantia polymorpha），以研究它们编码NBS的基因。令人惊讶的是，发现了两类新的编码NBS的基因。第一类新基因是从小立碗藓基因组中鉴定出来的，该类的一个典型成员在N端具有一个蛋白激酶（PK）结构域，在C端具有一个LRR结构域，形成了PK - NBS - LRR（PNL）的完整结构，让人联想到被子植物中的TNL和CNL类。第二类是从地钱基因组中发现的，该类的一个典型成员在N端具有一个α/β - 水解酶结构域，在C端也具有一个LRR结构域（水解酶 - NBS - LRR，HNL）。对内含子位置和相位的分析也证实了HNL和PNL类的新颖性，这体现在它们特定的内含子位置或相位特征上。涵盖所有四类编码NBS基因的系统发育分析显示，HNL、PNL和TNL类之间的关系更为密切，表明CNL类与其他类的差异更大。特定内含子的存在凸显了HNL、PNL和TNL基因的嵌合结构，并暗示它们可能是在早期陆地植物快速的谱系分化过程中通过外显子重排产生的。