About db

1. Data set infromation


Total 355,750 (231 Mb) transcriptome sequences from three lily sub species L. longiflorum (Easter Lily); L. formolongi (Sinnapal Lily) and L. longiflorum (White tower Lily). were generated from the cDNA library sequencing of leaf tissue with different biotic stress (Listed Below).
1. L. formolongi (Sinnapal Lily) transcriptome data set: Seeds of Lilium formolongi cv. ‘Sinnapal’ were sown in plastic pots contains sterilized potting mixture and kept in green house at 22 °C under 12 hours of light and 12 hours of darkness condition. Leaves of 120 days old plants were inoculated with Botrytis elliptica spore suspension culture. Then leaf sample from three plants were collected at five different time points (0 h, and 1, 2, 5, and 7 days) and immediately frozen in liquid nitrogen then stored at −80 °C until RNA extraction.

2. L. longiflorum (White tower Lily) transcriptome data set: Seeds of Lilum longiflorum cv. Napal and Lilum formolongi cv Shinnapal were sown in plastic pot contains sterilized potting mixture and kept in green house at 22 °C under 12 hours of light and 12 hours of darkness condition until flowering both species. After first flower flourish pollen from the L. formolongi cv shinnapal was use to pollination in to Lilum longiflorum cv. Napal. After pollination Botrytis elliptica spore suspension culture were sprayed in to the pollinated plant and also non pollinated Lilum longiflorum cv. Napal (as control). Then leaf samples from both pollinated and non pollinated were collected in the six time course (0h, 12h, 24h, 5days, 10 days and 20 days) and immediately frozen in liquid nitrogen then stored at −80 °C until RNA extraction.

3. L. longiflorum (Easter Lily) transcriptome data set: Seeds of four inbreed lines (L2-4, L2-28, L2-22, and L2-20) and their two hybrids L4-7 (L2-4 × L2-28) and L4-104 (L2-22 × L2-20) of Lilium longiflorum (Easter lily) were sown in plastic pots containing sterilized soil mixture for germination, and seedlings were produced in a green house at 22 °C under 12 hours of light and 12 hours of darkness. Leaves of 4 months aged seedlings were sampled with three replicates. The leaves of three replicates were combined for RNA extraction. Samples were immediately frozen in liquid nitrogen and stored at −80 °C in preparation for RNA-Seq analysis. 

Transcriptome sequencing and assembly cDNA libraries were constructed and sequenced by the Theragen Bio Institute, Republic of Korea (2nd Floor, B-dong, AICT, Gwanggyo Technovalley, Iui-dong, Suwon, gyeonggi-do, Republic of Korea) using the Illumina HiSeq 2500 platform. The quality of raw reads were determine by FastQC tool and denovo assemble performed by Trinity and RSEM tools. After that all the transcriptome were pooled together an assembled in to non-redundant lily unigenes using CAP3 (for more detail transcriptome sequencing and assembly, please visit http://210.110.86.160/Lidb/Lilidb_Home.html).

Table: Summary of the de novo assembly of three transcriptome datasets of Lilium spp.
Characteristics Easter Lily Sinnapal Lily White tower Lily
Raw read count 743,964,980 923,305,744 727,610,710
Total bases of Raw reads 75,140,462,980 46,626,940,072 73,488,681,710
GC% of Raw reads 51.74 51.97 48.51
Q30(%) 87.66 88.48 90.07
Clean read count 711,912,744 824924508 660,852,678
Total bases of clean reads 69,542,656,764 41,466,413,292 66,490,416,494
GC% of clean reads 51.36 52.45 49.21
Q30(%) 92.23 92.41 93.24
Unigene 179988 90115 85647
Size(bp) 113117791 60382994 57965647
Average Length (bp) 628 670 677

Table: Statistics of the CAP3 assembly for the generate non-redundant transcriptome

Item Counts
Total sequences analyzed 355750
CAP3 Contigs 54358
CAP3 Singlets 162410
Unigenes after CAP3 Assemble 216768
No of redundant sequence 138982
% of Redundant sequences 39.07
Maximum no of sequences per contigs 177
Minimum no of sequences per contigs 2
Unigenes length range (bp) 89-17422
Average length of unigenes (bp) 645

2. Pipeline of the SSR Marker development

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3. In silico characterization result


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Figure: In silico transferability and polymorphism: (a)No of markers are conserved among three data sets (b) Number and percentage of the transferable lily SSR markers to other monocots Musa, Foxtail, Rice and Sorghum (C)distribution of polymorphic marker among the different types of SSR markers based on inslico analysis results.

Contribution:
Planning: Dr. MK Biswas & Professor Ill-Sup Nou

Data base design & data generation:Dr. MK Biswas and Dr. Mita Bagchi

Web Interface Design: Dr. MK Biswas

CSS, Java and MySQL programming: Dhiman Biswas

PHP, HTML, JQuery programming:Dr. MK Biswas & Dhiman Biswas

Server side scripting, Site installation and maintenances: Dr. Sathishkumar Natarajan

Professor Ill-Sup Nou supervise entire project