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Zhang S, Sui Z, Chang L, Kang K, Ma J, Kong F, Zhou W, Wang J, Guo L, Geng H, Zhong J, Ma Q. Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform. Gene 2014; 537:285-93. [PMID: 24440238 DOI: 10.1016/j.gene.2013.12.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/27/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022]
Abstract
In this article, high-throughput de novo transcriptomic sequencing was performed in Alexandrium catenella, which provided the first view of the gene repertoire in this dinoflagellate based on next-generation sequencing (NGS) technologies. A total of 118,304 unigenes were identified with an average length of 673bp (base pair). Of these unigenes, 77,936 (65.9%) were annotated with known proteins based on sequence similarities, among which 24,149 and 22,956 unigenes were assigned to gene ontology categories (GO) and clusters of orthologous groups (COGs), respectively. Furthermore, 16,467 unigenes were mapped onto 322 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). We also detected 1143 simple sequence repeats (SSRs), in which the tri-nucleotide repeat motif (69.3%) was the most abundant. The genetic facts and significance derived from the transcriptome dataset were suggested and discussed. All four core nucleosomal histones and linker histones were detected, in addition to the unigenes involved in histone modifications.190 unigenes were identified as being involved in the endocytosis pathway, and clathrin-dependent endocytosis was suggested to play a role in the heterotrophy of A. catenella. A conserved 22-nt spliced leader (SL) was identified in 21 unigenes which suggested the existence of trans-splicing processing of mRNA in A. catenella.
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Sarmah R, Sahu J, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Sen P, Modi MK. ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs. Bioinformation 2012; 8:206-8. [PMID: 22419843 PMCID: PMC3302004 DOI: 10.6026/97320630008206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 02/11/2012] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED With the advent of high-throughput sequencing technology, sequences from many genomes are being deposited to public databases at a brisk rate. Open access to large amount of expressed sequence tag (EST) data in the public databases has provided a powerful platform for simple sequence repeat (SSR) development in species where sequence information is not available. SSRs are markers of choice for their high reproducibility, abundant polymorphism and high inter-specific transferability. The mining of SSRs from ESTs requires different high-throughput computational tools that need to be executed individually which are computationally intensive and time consuming. To reduce the time lag and to streamline the cumbersome process of SSR mining from ESTs, we have developed a user-friendly, web-based EST-SSR pipeline "EST-SSR-MARKER PIPELINE (ESMP)". This pipeline integrates EST pre-processing, clustering, assembly and subsequently mining of SSRs from assembled EST sequences. The mining of SSRs from ESTs provides valuable information on the abundance of SSRs in ESTs and will facilitate the development of markers for genetic analysis and related applications such as marker-assisted breeding. AVAILABILITY The database is available for free at http://bioinfo.aau.ac.in/ESMP.
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Affiliation(s)
- Ranjan Sarmah
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Jagajjit Sahu
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Budheswar Dehury
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Kishore Sarma
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Smita Sahoo
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Mousumi Sahu
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Madhumita Barooah
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Priyabrata Sen
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
| | - Mahendra Kumar Modi
- Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-
785013, Assam, India
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Chandrasekar A, Riju A, Sithara K, Anoop S, Eapen SJ. Identification of single nucleotide polymorphism in ginger using expressed sequence tags. Bioinformation 2009; 4:119-22. [PMID: 20198184 PMCID: PMC2828891 DOI: 10.6026/97320630004119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/10/2009] [Accepted: 06/08/2009] [Indexed: 12/05/2022] Open
Abstract
UNLABELLED Ginger (Zingiber officinale Rosc) (Family: Zingiberaceae) is a herbaceous perennial, the rhizomes of which are used as a spice. Ginger is a plant which is well known for its medicinal applications. Recently EST-derived SNPs are a free by-product of the currently expanding EST (Expressed Sequence Tag) databases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion/deletion) has led to a revolution in their use as molecular markers. Available (38139) Ginger EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script AutoSNP version 1.0 which has used 31905 ESTs for detecting SNPs and Indel sites. We found 64026 SNP sites and 7034 indel polymorphisms with frequency of 0.84 SNPs / 100 bp. Among the three tissues from which the EST libraries had been generated, Rhizomes had high frequency of 1.08 SNPs/indels per 100 bp whereas the leaves had lowest frequency of 0.63 per 100 bp and root is showing relative frequency 0.82/100bp. Transitions and transversion ratio is 0.90. In overall detected SNP, transversion is high when compare to transition. These detected SNPs can be used as markers for genetic studies. AVAILABILITY The results of the present study hosted in our webserver www.spices.res.in/spicesnip.
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Affiliation(s)
- Arumugam Chandrasekar
- Bioinformatics centre, Indian Institute of spice research, P.B.No.1701, Marikunnu P.O, Calicut -673012, Kerala, India
| | - Aikkal Riju
- Bioinformatics centre, Indian Institute of spice research, P.B.No.1701, Marikunnu P.O, Calicut -673012, Kerala, India
| | - Kandiyl Sithara
- Kandiyl House, Makkada (P.O), Kakkodi, Calicut – 673617. Kerala, India
| | - Sahadevan Anoop
- Ottankulam, Athicode (P.O), Palakkad (Dist), Kerala – 678554, India
| | - Santhosh J Eapen
- Bioinformatics centre, Indian Institute of spice research, P.B.No.1701, Marikunnu P.O, Calicut -673012, Kerala, India
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