广东桑和鲁桑叶绿体基因组高通量测序及基因注释分析

发布时间：2018-04-15 06:26

本文选题：广东桑 + 鲁桑　；参考：《西北农林科技大学》2017年硕士论文

【摘要】：叶绿体基因组的结构和组成较为保守且其片段的变异速率适中,适合用于研究植物的系统进化。桑树是在亚洲地区栽培的重要经济作物,本实验以广东桑(Morus atropurpurea Roxb)的栽培品种“一串红”和鲁桑(Morus multicaulis Perr)的栽培品种“日本胡橙”为实验材料,利用高通量测序技术对广东桑和鲁桑叶绿体基因组进行测序,研究桑属栽培种广东桑和鲁桑的叶绿体基因组结构,结合蒙桑(Morus mongolica Schneid)、印度桑(Morus indica Linne)和川桑(Morus notabilis Schneid)的叶绿体基因组,对桑属植物的亲缘关系进行研究。主要研究结果如下:1.广东桑和鲁桑叶绿体基因组是典型的四部分结构,广东桑叶绿体基因组总长159113 bp,两个反向互不重复区(IRa和IRb)均长25707 bp,被小单拷贝区(SSC)和大单拷贝区(LSC)分隔开,SSC和LSC的长度分别是87824 bp和19875 bp;鲁桑叶绿体基因组全长159154 bp,包括一对反向重复区长为25678 bp,一个大的单拷贝区长为87763 bp和一个小的单拷贝区长为20035 bp。2.广东桑和鲁桑的叶绿体基因组注释相同数量的基因,共有130个基因,包含85个蛋白编码基因(18个基因位于反向重复区)、8个核糖体RNA基因(r RNA)和37个转运RNA基因(t RNA)。且广东桑和鲁桑中含有内含子的基因的数量是一样的,均为24个,其中有22个基因只包含1个内含子(包括12个蛋白编码基因、8个t RNA基因和2个假基因),另外有2个基因含有2个内含子,分别是clpP基因和ycf3基因,广东桑和鲁桑叶绿体基因的数目、种类以及CG含量与其他的桑属植物相类似。3.通过生物信息学分析,广东桑有83个简单重复序列(SSR)位点,单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序的个数分别是60个、8个、3个、10个和2个,未发现六核苷酸重复序列,数量最多的重复序列是A/T和AT/TA,这些重复基序占总数的79.8%;而鲁桑共搜索到82个SSR位点,单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序分别有63个、7个、2个、9个和1个,同样未发现六核苷酸,单核苷酸重复基序在鲁桑的叶绿体基因组总重复基序中占76.8%。所有的单核苷酸和14个SSR的多核苷酸由A和T组成。对SSR位置进行探讨,10个核苷酸重复基序位于编码区,其余的位于非编码区。大多数位点都偏向由A或T组成。4.用MEGA 6.0软件通过最大似然法(ML)和邻近法(NJ)对包括5个桑属物种在内的27个物种的叶绿体全基因组序列进行聚类分析,桑属物种聚成一组,其中广东桑和蒙桑聚成一个小组,再和鲁桑聚在一起,印度桑和川桑聚成一个小组。研究结果对于叶绿体基因组工程研究、桑属种间的分子标记开发和优良品种培育具有一定参考价值。
[Abstract]:The structure and composition of chloroplast genome are conserved, and the variation rate of chloroplast genome is moderate, which is suitable for phylogeny of plants.Mulberry is an important economic crop cultivated in Asia. The cultivars of Morus atropurpurea Roxb and Morus multicaulis Perrn in Guangdong Province were used as experimental materials.The chloroplast genomes of Morus mongolica mongolica, Morus indica Linnei and Morus notabilis Schneidi were sequenced by high-throughput sequencing technique. The chloroplast genomes of Morus mongolica Schneidi and Morus notabilis Schneidi were studied.The relationship of mulberry plants was studied.The main results are as follows: 1.The chloroplast genome of Guangdong mulberry and Lu mulberry is a typical four-part structure.The total length of chloroplast genome of Guangdong mulberry is 159113 BP, and the length of two reverse non-duplicated regions is 25707 BP. The length of chloroplast LSC separated by small single copy region and large single copy region is 87824 BP and 19875 BP, respectively, while the length of chloroplast genome is 19875 BP.159154 BP, including a pair of reverse repeat region length of 25678 BP, a large single copy region length of 87763 BP and a small single copy region length of 20035 bp.2.There are 130 genes in the chloroplast genome of Guangdong mulberry and Lu mulberry, which contain 85 protein coding genes (18 genes located in reverse repeat region, 8 ribosomal RNA genes) and 37 transporter RNA gene tRNAs.And the number of intron genes in Guangdong mulberry and Lu mulberry were the same, which were both 24.Among them, 22 genes contain only one intron (including 12 protein coding genes, 8 t RNA genes and 2 pseudogenic genes), and the other 2 genes contain 2 introns, which are clpP gene and ycf3 gene, respectively.The number, species and CG content of chloroplast genes in Mulberry and Lu-mulberry of Guangdong Province were similar to those of other mulberry plants.According to bioinformatics analysis, there are 83 SSRs in Guangdong mulberry. The number of single nucleotide, dinucleotide, trinucleotide, tetranucleotide and pentanucleotide repeat motifs are 60, 8, 3, 10 and 2, respectively.Six nucleotide repeats were not found, and the largest number of repeats were A / T and AT / T, which accounted for 79.8 percent of the total number of repeats, while in Rusan 82 SSR sites, single nucleotides, dinucleotides, trinucleotides, and dinucleotides were found.There were 63, 7, 2, 9 and 1 quanucleotide repeat motifs, respectively. The single nucleotide repeats accounted for 76.8% of the total repeat motifs in the chloroplast genome.All single nucleotides and 14 SSR polynucleotides are composed of A and T.The location of SSR was studied. Ten nucleotide repeat motifs were located in the coding region and the others were in the non-coding region.Most sites tend to be composed of A. or T.The chloroplast whole genome sequences of 27 species, including 5 mulberry species, were analyzed by MEGA 6.0 software by maximum likelihood method (MLL) and adjacent method (NJ). Mulberry species were clustered into a group, among which Guangdong mulberry and Mongolian mulberry gathered as a group.Then, together with Rusan, India and Kawasang get together in a group.The results are valuable for the development of interspecific molecular markers and breeding of fine varieties in chloroplast genome engineering.
【学位授予单位】：西北农林科技大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S888.2

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