Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates.
Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates.
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DOI：
10.1093/g3journal/jkab299
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发表时间：
2021-12-08
期刊：
影响因子：
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通讯作者：
Sumner-Rooney L
中科院分区：
文献类型：
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作者：
Harper A;Baudouin Gonzalez L;Schönauer A;Janssen R;Seiter M;Holzem M;Arif S;McGregor AP;Sumner-Rooney L
全基因组复制（WGD）在动物进化过程中多次发生，包括脊椎动物、硬骨鱼、马蹄蟹和蛛形纲动物的谱系。这些戏剧性的事件最初产生了丰富的新遗传物质，通常随后是广泛的基因丢失。然而，似乎发育基因如同源框基因、信号传导途径组分和microRNA在WGD后经常被保留为重复（所谓的同源物）。这不仅为WGD提供了最好的证据，也为研究其进化后果提供了机会。尽管这些基因在脊椎动物WGD的背景下得到了很好的研究，但在现存的蛛形纲动物中的类似比较是不完整的。我们对两种蜘蛛和两种amblypygid物种的胚胎转录组进行了测序，并调查了三个重要的基因家族，Hox，Wnt和frizzled，跨越这些和12个现有的转录组和基因组资源的chelicerates。我们报告了广泛保留的假定ohnologs，进一步支持祖先的arachnopulmonate WGD。我们还发现了证据的一致的进化轨迹在Hox和Wnt基因库在三个六个arachnopulmonate订单，与订单间的变化，在保留特定的旁系同源。我们确定了蜘蛛的主要分支之间的变化，能够更好地重建蜘蛛，amblypygids和蝎子的基因复制和损失的年表。这些见解揭示了在arachnopulmonates的发展工具包的演变，突出了谱系内的比较方法的重要性，并为未来的研究提供了大量新的转录组数据。
Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.