大麻状罗布麻的全基因组分析和SSR标记开发

Whole Genome Sequencing and Development of SSR Markers in Apocynum cannabinum

大麻状罗布麻是重要的经济和生态作物,由于基因组数据匮乏和分子标记少而限制其遗传研究工作的开展。本研究利用Illumina测序平台对大麻状罗布麻的基因组大小进行测定,通过生物信息学方法对其基因组杂合度和重复序列等基本信息进行预估,并做了基因组的初步组装,在此基础上对其基因组序列进行了SSR查找。研究结果表明,总测序量为31.94 Gb,测序质量正常(Q20≥90%,Q30≥85%),与NCBI核苷酸数据库(NT)比对显示样本不存在外源污染;K-mer分析(K=17)结果显示,大麻状罗布麻基因组大小为239.02 Mbp,杂合率为0.56%,重复序列占全基因组比例为36.72%,初步预估大麻状罗布麻基因组为复杂基因组;采用K-mer=41进行基因组初步组装,共获得273336条contigs,N50为3838 bp,总长为222723253 bp,进一步将contigs进行连接、延长,组装得到224587条scaffolds,N50为6421 bp,总长为226378236 bp;此外,对基因组数据进行SSR分子遗传标记分析,共鉴定出117511个SSR,不同类型核苷酸重复差异较大,单核苷酸重复最多,六核苷酸重复最少。该研究为后续全基因组de novo测序及组装策略提供依据。

Apocynum cannabinum L.is an important economic and ecological crop.Genetic studies on this crop remains largely behind due to the un-availability of genome reference and limited amount of molecular markers.In this study,we performed a whole genome sequencing of A.cannabinum L.by sequencing technology(Illumina),and analyzed the ratios of heterogeneity and repetitive elements,followed by exploration of SSR markers.A total of 31.94 Gb high-quality sequences(Q20≥90 and Q30≥85%)have been generated.By searches with NCBI nucleotide database(NT),no exogenous contamination in the sample was detected.De novo assembly and K-mer analysis revealed a genome size of 239.02 Mbp,with 0.56%heterozygosity and 36.72%of repetitive sequences.273336 contigs with a N50 of 3838 bp in length have been detected,and the total length was 222723253 bp.224587 scaffolds were further assembled,with a N50 of 6421 bp in length,and the total length was 226378236 bp.By predicting for the simple sequence repeats(SSR),117511 have been detected potentially for exploring SSR markers.Of all SSR categories,the mononucleotide and hexanucleotide repeat units formed the largest and the least categories,respectively.Thus,this work generated a sequence dataset that might be useful source for future de novo assembling of A.cannabinum L.genome.