基于基因组高通量测序方法精准鉴定植物遗存——河南崔寨遗址案例

Accurate identification of archaeobotanical remains based on high-throughput genome sequencing methods:A case study from Cuizhai site of Henan Province

本研究尝试利用基因组高通量测序方法精准鉴定植物遗存,遗存来自河南周口市崔寨遗址。本项工作提取了植物遗存材料中的基因组DNA,使用Illumina测序平台对该植物遗存的基因组进行浅层测序,并拼装其质体基因组,然后将所得的质体基因组片段通过BLAST进行序列比对,获得了该材料的物种信息。为校验基因组高通量测序的结果,进行了植物形态学鉴定,首先结合植物遗存出土情况及其在显微镜下观察到的结构特点,对样品进行初步的物种判断,然后结合BLAST序列比对和形态学初步判断的结果,采集同一类群的活植物,进行两类材料的植物形态学解剖实验,将二者的形态进行对比;随后,将现生植物组织用NaOH溶液浸泡,用于模拟其在自然状态下的降解过程,并在显微镜下观察其形态结构。根据高通量测序和形态学两方面证据,将该植物遗存鉴定为禾本科植物芦苇(Phragmites australis)的根,并测得该植物遗存的14C年代为660±30 a B.P.。由此推测,在距今约700年前,自然分布的芦苇从崔寨遗址2019LCⅠ区M1墓室坍塌的顶部进入,扎根深入墓葬器皿中,得以保存至今。研究显示,利用基因组高通量测序的方法可以对出土的植物遗存进行精准物种鉴定。基因组高通量测序和形态鉴定方法的综合运用,可作为精准鉴定出土植物遗存的新方法。

In this study,we tried to explore new methods of high-throughput genome sequencing to accurately identify a plant remains unearthed from the Cuizhai site(33°52'37.09″N,115°15'08.81″E),Henan Province.We extracted genomic DNA from this plant remains,and used Illumina sequencing platform to perform shallow sequencing of the whole genome of the material.Subsequently,the obtained sequencing data was used to assemble the plastid genome.By means of sequence alignment,the obtained plastid sequence fragments are subjected to BLAST alignment to obtain species information of the material.To verify the results of high-throughput genome sequencing,we checked the morphological characters of the plant remains under the microscope and made preliminary identification.Combining the results from BLAST alignment and preliminary morphology identification,we collected modern plants of the same species,and carried out morphological anatomy experiments of the two types of materials.Subsequently,the modern plant tissues were soaked in NaOH solution to simulate the degradation process in natural state,and the morphological characters were observed.Based on high-throughput sequencing and morphological evidence,we identified the plant remains as the root of reed(Phragmites australis).Via 14C,we determined the age of the plant remains was 660±30 a B.P.We speculated that,ca.700 years ago,the naturally distributed reeds entered from the collapsed top of the M1 tomb in the 2019 LCⅠarea of the Cuizhai site,took root deep into the porcelain jar of the site,and have been preserved till now.This study shows that the application of high-throughput genome sequencing methods can accurately identify the species of unearthed plant remains.The comprehensive application of high-throughput genome sequencing and morphological identification way could be a new method for accurate identification of the archaeological plant remains in the future.