“ Genome and transcriptome sequencing of coriander (Coriandrum sativum L.) to reveal its genome architecture.”2508
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Date
2013
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JAU,JUNAGADH
Abstract
Coriander (Coriandrum sativum L.) is an important spice and medicinal plant having a prime position in flavoring food. It is a cross pollinated annual herb belongs to family Apiaceae. The basic chromosome number of the genus Coriandrum is x=11, and C. sativum L. is a diploid with 2n=22. The different parts of this plant contain monoterpenes, α-pinene, limpnene, γ-terpinene, p-cymene, borneol, citronellol, camphor, geraniol, coriandrin, dihydrocoriandrin, coriandrons A-E, flavonoids and essential oils. Linalool is the main volatile compound in coriander seeds.
For the measurement of the genome size, flow cytometer (Accuri C6) was used, found approximately 1.5 Gb. In genome sequencing after completions of sequencing run the total raw sequence generated by Ion S5 sequencer was 18,343,973 and 83,491,312bp followed by first and second lane. Total raw data was 22.8 Gb. Raw data (Reads) generated from two different runs for coriander were assessed for quality check using FastQC. After trimming of reads average read length was 315 and 189 bp. The de novo assembly (using CLC genomic workbench V 8.2) yielded assembled reads of 81,261,231 and number of contigs was 175,275
Total 121 unspecified repeats were found using repeat masker along with transposable elements found in coriander genome. In our study unspecified elements were found BNINTMO BoSB6D, BoSB7A, BvL1, BvL1-2, CALYPSHAN2_I_MT, CAULIV1. Transposable elements like COP10_I_MT, COP12_I_MT, COP16_I_MT, Copia10-VV_LTR and also other were found as listed in table. In total 76069 with highest number of hexa nucleotides were found in Gujarat coriander 2 genome. The highest numbers of SSRs were hexa nucleotide about 23% and 18% hepta
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nucleotides contribution to all SSRs followed by penta nucleotide 16 % and 14% di and tetra nucleotides in respective genome.
In transcriptome study raw data (reads) from sequencing (NGS) was assessed through FASTQC quality control tool in which all samples (leaf, flower and seed) having good quality sequence for further analysis. After trimming of raw reads, total of 759,382,622 in leaf 371,962,963 in flower and 362,392,162 in seed sample with a mean length of 104.32bp, 150.42bp and164.82bp in leaf, flower and in seed. The de novo assembly (using trinity) yielded assembled reads of 109116bp.
Gene expression level was differentiated among three groups (Leaf, flower and seed). To study gene expression pattern and also validation of the RNA sequencing technique, 15 primers were selected based on their expression for quantitative RT PCR. The GOLD-like protein and shows up regulation in leaf while Fimbrin-like protein shows Down regulation in flower and leaf. In seed chaperone and transcription factor 22 genes are up regulate, while MADS-box protein was down regulated. During flower developmental stage transcription activator GLK1 was up regulated and MADS box transcription_factor was down regulated.
Total 4232 SSRs were identified with Tm and GC % range of 56–62 °C and 40-70, respectively. Length of SSR primer is between 17-27 bp with 100-250bp of product size range. During this study SSR of Guj-Coriander 2 having total number 204 SSRs identified, validatation of the SSR primers in 14 different varieties of coriander were Gujarat coriander 1, Gujarat coriander 2, GDLC, Punjab Sugandham, Loca; Kalmi (Raj), PAU-150, Co-1, Co-2, Co-3, Rcr-435, Rcr-436, Rcr-446, Rcr-480, Rcr-728.Total of 204 primers were used. Out of 204 primer 88 primers are amplified a total 164 band. The largest amplicone of 1608 bp was amplified by SSR primer COR 3 and smallest fragment of 98 bp was found with SSR primer COR62.
In the present study, the qualitative analysis of ethanolic extract of coriander was carried out using GC-MS for the identification of bioactive components. The finger prints of the compound were identified from The National Institute of Standard and Technology (NIST) library database. The result of GC-MS analysis of coriander revealed the existence of sugars, organic acids, Vitamins and other bioactive compounds.
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BIOTECHNOLOGY