睡莲基因组图谱构建与细胞器RNA转录后加工

	睡莲基因组图谱构建与细胞器RNA转录后加工; Phased chromosome-level genome assembly and organellar post-transcriptional RNA processing of Nymphaea
	贺正山
导师	李德铢
摘要	Water lilies (Nymphaea L.) are highly favored aquatic ornamental plants found nearly every botanical garden for their aesthetic beauty, and are of high cultural and economic importance. Nymphaea is the most speciose genus in Nymphaeaceae, one of the three families of Nymphaeales which occupies a critical evolutionary position, as sister to all other extant angiosperms apart from Amborella (Amborellales). Nymphaea has a cosmopolitan distribution with about 50 species and about 2000 cultivars. Nymphaea forms hermaphroditic flowers which are self-compatible and could hybrid at the intra- or inter-subgeneric levels. Nymphaea is of varied ploidy, with small chromosomes. Genomics is powerful in solving speciation and evolution, genetic variation and breeding new varieties. As the Third Generation Sequencing platforms develope, and it is time to get the reference genome sequences of Nymphaea for genetic, evolutional and development studies. In this thesis, we chose a hardy waterlily cultivar with fragrant and yellow flowers, pollution-resistance and strong growth to assemble and annotate its nuclear and organelle genomes. The posttranscriptional process of organelle RNA was also investigated. By ultilizing morphological and molecular identification, we proved that the sequencing material was Nymphaea 'Joey Tomocik', with N. odorata as maternal, andN. mexicana as paternal. After root tip squash, the chromosome number of N. 'Joey Tomocik' was counted to be about 56. The parental plants had the same karyotype, 2n=4X=56. The genome size of N. 'Joey Tomocik' was determined to be about 690 Mbp by flow cytometry and K-mer analysis of genome survey sequencing data. The genome of N. 'Joey Tomocik' was sequenced by PacBio platforms. More than 1.25 Gbp were assembled by different softwares using long reads only, all with contig N50 larger than 3 Mbp. To validate whether both subgenomes were assembled, short reads of both parents were added. By using Trio binning of CANU, two pesudo-haploytes, named MXG and XSL, were assembled successfully, with assembly sizes of about 493 Mbp and 764 Mbp, respectively. The total size of genomes of two pesudo-haploytes was equal to the assembly (1.258 Gbp) by CANU using long reads alone. After scaffolding by Hi-C, 1057 contigs were ordered into 56 chromosomes with total size of 1.231 Gbp. After assessing the assembly by many kinds of tools, it was confirmed that we got a chromosome-level assembly with high accuracy and completeness. After annotation, 45.6% of the genome is repeat sequences, and 68,889 protein coding genes are predicted. The genomes of N. 'Joey Tomocik' and N. colorata are highly collinear, as well as the subgenomes within N. 'Joey Tomocik', which were diverged 7.9 Mya. We successfully assembled the chloroplast and mitochondrial genomes of N. 'Joey Tomocik' (159,968 bp and 335,042 bp, respectively). By accurately mapping Iso-seq reads to organelle genomes, annotations by in-silico approach were refined, and more com
	2021-11
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74585
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	贺正山. 睡莲基因组图谱构建与细胞器RNA转录后加工, Phased chromosome-level genome assembly and organellar post-transcriptional RNA processing of Nymphaea[D],2021.

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