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Title
[Presentation/2016] Plant Genome Era: Understanding plant genomes from the sequences
Contents
Genome, defined as a blend of gene and chromosome, represents whole nucleotide sequences of one organism. Arabidopsis thaliana genome (119.15 Mbp) was fully sequenced by Sanger sequencing method as the first plant genome. After this genome, two rice (Oryza sativa subsp. japonica and O. sativa subsp. indica) genomes were released (374.47 Mbp and 395.82 Mbp, respectively). Consequently, tree genomes, Populus trichocapa (434.13 Mbp) and Vitis vinifera (486.27 Mbp), were also successfully sequenced. In 2009, cucumber (Cucumis sativus; 243.57 Mbp) genome was sequenced and assembled with the aid of one of next generation sequencing (NGS) technologies (Illumina), which decreased sequencing cost dramatically. It probed that plant genome can also be analyzed with the low cost. Currently, more than 100 plant genomes have been sequenced; however, there is no repository for all plant genome sequences, which is a critical huddle for analyzing all available plant genomes. A standardized plant genome database (http://www.plantgenome.info/) has been established. Currently, 118 plant genomes (95 species) were collected from NCBI, Phytozome, Ensembl, as well as many independent plant databases. Total length of 118 genomes is 130.39 Gbp (1.11 Gbp on average) and total number of ORFs is 4,691,060 from 112 genomes (41,884 ORFs per genome). Ninety-five species consists of 12 green algal species, three mosses, one fern, three Gymnosperm species, and 78 Angiosperm species. Six Angiosperm families (Poaceae, Solanaceae, Rosaceae, Brassicaceae, Salicaceae, and Fabaceae) cover 72 genomes from 49 species, reflecting that many of sequenced species are economic crops, fruits, or horticultural species. The smallest genome except green algal species is Capsella grandiflora (105.35Mb) and the largest one is Pinus lambertiana (34.08 Gbp), which is 323 times than that of C. grandiflora. Total size of three sequenced Gymnosperm genomes is 72.20 Gbp (55.37\%). 12 out of 118 genomes (10.17\%; called as large plant genomes) are more than 1 Gbp long, indicating that large size plant genomes are still difficult to sequence. As expected, there is no significant correlation between genome length and number of ORFs; while GC ratio of plant genomes is correlated with taxonomy. For example, GC ratio of 10 green algal genomes shows from 52.90\% to 67.14\%; while that of 21 monocot genomes (Poaceae and Araceae) are from 40.49\% to 46.89\% and 76 dicot genomes displays 32.31\% to 39.56\%. Throughout these analyses, 130 Gbp plants genome sequence is not just nucleotides but new indicators to understand plants in various aspects.
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Create date
2018-09-09 19:40:02
Lastupdate date
2018-09-09 19:50:14
Creator
starflr (Jongsun Park)
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