Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.
Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.
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从亚美尼亚南部 Areni-1 洞穴出土的中世纪小米中恢复叶绿体基因组。
DOI：
10.1038/s41598-022-17931-4
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发表时间：
2022-09-07
影响因子：
4.6
通讯作者：
Zhang, Heng
中科院分区：
文献类型：
--
作者：
Richards, Stephen M.;Li, Leiting;Breen, James;Hovhannisyan, Nelli;Estrada, Oscar;Gasparyan, Boris;Gilliham, Matthew;Smith, Alexia;Cooper, Alan;Zhang, Heng
黍至少在7000年前，中国北方人就开始驯养了，并在欧亚大陆的许多地区得到了广泛的应用。其中一个地点是Areni-1，这是亚美尼亚南部的一个考古洞穴遗址，大量的考古植物材料通过干燥保存完好。在Areni-1发现的丰富的植物材料包括形态学鉴定的P. miliaceum谷物和14 C可追溯到中世纪时期（873 ± 36 CE和1118 ± 35 CE）。为了调查Areni-1小米的人口统计和进化历史，我们使用古代DNA提取，杂交捕获富集和高通量测序从中世纪谷物中组装了三个叶绿体基因组，然后将这些序列与50个现代P. miliaceum叶绿体基因组进行比较。总体而言，叶绿体基因组包含少量的多样性与驯化加入分离的最多5个SNP和人口统计学上的推断可以。然而，在叶绿体基因组中，叶绿体基因组分成两个分支，类似于已经报道的来自粟粒拟青霉的核DNA。两个野生（未驯化）种质的叶绿体基因组中含有相对大量的变异体，11个SNP，在驯化种质中没有发现。这些结果表明，来自考古遗址的粟粒可以保存DNA至少1000年，并作为研究这种谷类作物驯化的遗传资源。
Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and14C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.
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DOI：
10.1007/978-3-319-45105-3_4
发表时间：
2017-01-01
期刊：
GENETICS AND GENOMICS OF SETARIA
影响因子：
--
作者：
Diao, Xianmin;Jia, Guanqing
通讯作者：
Jia, Guanqing
影响因子：
2.7
作者：
Chomczynski, P;Mackey, K;Wilfinger, W
通讯作者：
Wilfinger, W
影响因子：
0.9
作者：
Christian, D
通讯作者：
Christian, D
影响因子：
4.6
作者：
Armbrecht L;Hallegraeff G;Bolch CJS;Woodward C;Cooper A
通讯作者：
Cooper A
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T