Sequencing the genomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro

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1 Sequencing the genomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro Philip Morris International R&D, Philip Morris Products S.A., Neuchatel, Switzerland

2 Introduction Nicotiana sylvestris and Nicotiana tomentosiformis are diploids (2n=12) originating from overlapping regions of South America They probably diverged early in the evolution of genus Nicotiana which split from Symonanthus around 15 Myr ago 1 Their 1C genome size is estimated at 2.65 Gb 1, about 3 times the size of the tomato and the potato genomes 1. Renny-Byfield, S. et al Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs. Mol. Biol. Evol. 28:2843. Page: 2

3 Introduction Modern descendants of the maternal and paternal donors that formed tobacco 1 N. sylvestris ancestor 2n=24 N. tomentosiformis ancestor 2n=24 The determination of their genome and transcriptome will contribute to the assembly and annotation of the tobacco genome and transcriptome N. tabacum 2n=4x=48 1. Leitch, I.J. et al The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot Apr;101(6): Page: 3

4 Genomes sequencing and assembly strategy DNA isolation - Leaves Library preparation - Paired ends - Mate pairs Sequencing Illumina 2x100 bp Quality filtering and trimming Superscaffolding Scaffolding - SOAPdenovo Contig creation - SOAPdenovo related species Tobacco WGP physical map Page: 4

5 Genome libraries Nicotiana sylvestris Total coverage of 94x Library type Read size Insert size Cleaned reads Expected coverage Paired ends 2x b x Paired ends 2x b x Paired ends 2x100 1 kb x Mate pairs 2x100 3 kb x Mate pairs 2x100 4 kb x Mate pairs 2x100 4 kb x Using the 31-nucleotide depth distribution, the genome size is estimated at 2.58 Gb. Page: 5

6 Genome libraries Nicotiana tomentosiformis Total coverage of 146x Library type Read size Insert size Cleaned reads Expected coverage Paired ends 2x b x Paired ends 2x b x Paired ends 2x b x Paired ends 2x b x Paired ends 2x100 1 kb x Mate pairs 2x100 3 kb x Mate pairs 2x100 5 kb x Using the 31-nucleotide depth distribution, the genome size is estimated at 2.14 Gb. Page: 6

7 Genome assemblies N. sylvestris N. tomentosiformis Sequences Average length (bp) Maximum length (bp) N50 length (bp) Total length (bp) Undefined bases (7.8%) (2.7%) Genome coverage 82.9% 71.6% Using the S/T regions of the tobacco WGP physical map N. sylvestris N. tomentosiformis Superscaffolds Components N50 length (bp) Page: 7

8 Repeat content Species specific repeat library created using RepeatScout on sequences of at least 200kb. Repeat classification using blast against known repeat elements. Repeat content estimation using RepeatMasker with the RepeatScout, TIGR Solanaceae and SOL eudicot repeat libraries. Page: 8

9 Repeat contents 72-75% of the sequenced genome consists of repeats. 625 and 425 Mb of unmasked DNA for N. sylvestris and N. tomentosiformis. Repeat element N. sylvestris N. tomentosiformis LINE (0.3%) (0.2%) SINE (0.2%) (0.3%) LTR/Copia (9%) (13%) LTR/Gypsy (21%) (20%) LTR/Others (8%) (5%) Transposons (1.5%) (1%) Retrotransposons (10%) (13%) Simple repeats (0.2%) (0.3%) Low complexity (0.5%) (0.6%) Others (13%) (15%) Total (72%) (75%) Page: 9

10 Transcriptome sequencing and assembly strategy RNA isolation - Leaves - Roots -Flowers Library preparation - Paired ends Sequencing Illumina 2x100 bp 3 biological replicates Quality filtering and trimming ORF finding Isoform prediction - cufflinks/cuffmerge Annotation Read mapping - bowtie/tophat - BLAST - InterPro Scan (GO terms) - EFICAz (EC number) Page: 10

11 Transcriptome assemblies Nicotiana sylvestris Tissue Transcripts Shortest Longest Median Roots Leaves Flowers Nicotiana tomentosiformis Tissue Transcripts Shortest Longest Median Roots Leaves Flowers Page: 11

12 Mutual best BLAST hits against UniProt Proteins predicted by Trinity ORF finding program Minimum length of 100 amino acids Mutual blast against UniProt plants collection Filter pairs by e-value of less than 1E-10 in either direction Select proteins with mutual best hits Best blast hit Best blast hit Predicted protein UniProt protein Predicted protein Best blast hit Page: 12

13 Mutual best blast hits against UniProt N. sylvestris N. tomentosiformis Coverage of reference Coverage of query 82% of the transcripts have homologous UniProt sequences, but some of them are only partially covering the reference sequence. Page: 13

14 GO term enrichment GO term enrichment for each species against the pooled set of GO terms using GOStats. Only small and not highly significant changes in gene composition. N. sylvestris: defense response function N. tomentosiformis: core metabolic functions, protein phosphorylation Phenotypic difference more likely to be regulatory than due to loss or gain of genes. Page: 14

15 Transcriptome overlap OrthoMCL was used to define clusters of orthologous and paralogous genes between species: N. sylvestris N. tomentosifomis Tomato Arabidopsis And between the root, leaf and flower transcriptomes of N. sylvestris and N. tomentosifomis. Page: 15

16 Transcriptome overlap between species ~7 000 clusters are shared between all species. ~3 600 clusters are specific to Nicotiana. ~2 800 clusters are specific to Solanaceae. Page: 16

17 Transcriptome overlap in N. sylvestris ~ clusters are shared. ~3 500 clusters are specific to flower. ~2 000 clusters are specific to root. ~1 800 clusters are specific to leaf. Page: 17

18 Transcriptome overlap in N. tomentosiformis ~ clusters are shared. ~3 400 clusters are specific to flower. ~2 600 clusters are specific to root. ~1 900 clusters are specific to leaf. Page: 18

19 Conclusions Nicotiana sylvestris and Nicotiana tomentosiformis have been sequenced at a coverage of about 100x and 150x respectively. 83% of the N. sylvestris genome covered. 72% of the N. tomentosiformis genome covered. the tobacco WGP physical map can be used to superscaffold the assembly. Between and transcripts are identified by mapping of RNA-seq data. More than 80% have homologs in UniProt. Page: 19

20 Conclusions About clusters of orthologous and paralogous genes genes are shared between root, leaf and flower clusters specific to flowers About clusters of orthologous and paralogous genes are shared between N. sylvestris, N. tomentosiformis, tomato and Arabidopsis. About clusters of orthologous and paralogous genes specific to Nicotiana species. The obtained genomes and transcriptomes will contribute to the assembly and annotation of the tobacco genome. Page: 20

21 Acknowledgments James Battey Sonia Ouadi Lucien Bovet Simon Goepfert Nicolas Bakaher Manuel C. Peitsch Nikolai V. Ivanov Page: 21

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