An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa

First author: Djivan Prentout; Affiliations: Université Lyon (里昂大学): Villeurbanne, France

Corresponding author: Gabriel A.B. Marais

Cannabis sativa–derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY Chromosomes, and only females (XX) are useful for THC production. Identifying the sex chromosome sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects have failed to do so. Moreover, as dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study, as little is known about old plant sex chromosomes. Here, we RNA-sequenced a C. sativa family (two parents and 10 male and female offspring, 576 million reads) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified the largest chromosome pair being the sex chromosomes. We found that the X-specific region (not recombining between X and Y) is large compared to other plant systems. Further analysis of the sex-linked genes revealed that C. sativa has a strongly degenerated Y Chromosome and may represent the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large, highly divergent nonrecombining regions, yet still be roughly homomorphic.

源自于大麻的四氢大麻酚在全球范围内的产量都在快速的上升。大麻是雌雄异株的植物，具有XY性染色体，而且只有雌株（XX）用于四氢大麻酚的生产。鉴定性染色体序列将有助于早期的性别选择，有利于更加便捷的作物管理。然而，大麻基因组项目并未成功鉴定出大麻的XY染色体。此外，大麻科植物祖先物种属于雌雄异株（doi: 10.1093/aob/mcy159），因此大麻的性染色体可能很古老，具有很高的研究价值，目前对于古老植物性染色体的了解并不多。本文中，作者对大麻家族进行了RNA测序，一对父母本以及10个雄性和雌性子代植株，共获得了576百万个reads，利用一种概率方法SEX-DETector（doi: 10.1093/gbe/evw172）来对所有的大麻基因进行分离分析。作者鉴定了超过500个性别连锁的基因。将这些鉴定到的性别连锁基因比对到大麻的基因组组装，作者发现大麻最长的那一对染色体为一对性染色体。作者发现X染色体特异的序列区域，即X与Y染色体之间不存在重组的区域，该区域与其它的植物系统能够很好的比对上。进一步对于性别连锁基因的分析，作者发现大麻的Y染色体已经严重退化了，可能是目前已知的最古老的植物性染色体系统。本文的研究揭示了一个古老的植物性染色体具有一段很长的、高度分化的非重组区域，并且这对性染色体还是同型的。

通讯：Gabriel A.B. Marais (https://lbbe.univ-lyon1.fr/-Marais-Gabriel-.html?lang=en)

个人简介：2002年，里昂大学，博士；2002-2004年，爱丁堡大学，博士后。

研究方向：动植物性染色体的演化；植物性系统的演化；植物基因组与表型演化。

doi: 10.1101/gr.251207.119

Journal: Genome Research

Published online: February 07, 2020