De-novo transcriptome assembly for discovery of putative microsatellite markers and transcription factors in black pepper (Piper nigrum)

被引:0
作者
Negi, Ankita [1 ]
Jasrotia, Rahul Singh [1 ]
Jaiswal, Sarika [1 ]
Angadi, U. B. [1 ]
Iquebal, M. A. [1 ]
George, Johnson [2 ]
Rai, Anil [1 ]
Kumar, Dinesh [1 ]
机构
[1] ICAR IARI, New Delhi, India
[2] ICAR Indian Inst Spices Res, Kozhikode 673012, Kerala, India
来源
INDIAN JOURNAL OF AGRICULTURAL SCIENCES | 2019年 / 89卷 / 07期
关键词
Black pepper; de novo assembly; Markers; RNA-sequence; Transcription factors; ANTIOXIDANT; PATTERNS;
D O I
暂无
中图分类号
S [农业科学];
学科分类号
09 ;
摘要
Black pepper (Piper nigrum L.) (2n= 52; Piperaceae), is a perennial, trailing woody flowering vine having global importance with widespread dietary, medicinal, and preservative uses. It is one of the highly traded high cost spice germplasms cultivated for its fruit. Unlike model species, the whole genome sequence information and genomic resources of black pepper are still unavailable in public domain. Crop production is highly affected by abiotic and biotic stresses. Hence transcriptome profiling has permitted a significant enhancement in discovery and expression profiling of genes and functional genomic studies in black pepper. Stress responsive transcriptomic data of various black pepper genotypes were obtained from public domain (SRA database, NCBI) for the de novo transcriptome assembly, identification of transcription factors and mining of putative simple sequence repeat markers. De novo transcriptome assembly was done with SOAP denovo-trans assembler, which generated 53690 transcripts. A total of 14005 transcription factors with BLAST and 39685 without BLAST hits were identified. A total of 4770 putative SSR markers were identified using de novo transcriptome assembly. Myeloblastosis (MYB) related proteins, Basic helix-loop-helix (BHLH), NAC, WRKY and ERF transcriptional factors found in this study are reported to be associated with plant tolerance against stress condition. These SSR markers can be valuable and facilitate advancements in genetic and molecular studies in the endeavour of better productivity of P. nigrum germplasm, especially in the era of rising abiotic stress.
引用
收藏
页码:61 / 65
页数:5
相关论文
共 23 条
[1]   Efficient regeneration and antioxidant potential in regenerated tissues of Piper nigrum L. [J].
Ahmad, Nisar ;
Fazal, Hina ;
Abbasi, Bilal Haider ;
Rashid, Muhammad ;
Mahmood, Tariq ;
Fatima, Nighat .
PLANT CELL TISSUE AND ORGAN CULTURE, 2010, 102 (01) :129-134
[2]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[3]  
[Anonymous], 2017, FAOSTAT PROD CROPS M
[4]   Trimmomatic: a flexible trimmer for Illumina sequence data [J].
Bolger, Anthony M. ;
Lohse, Marc ;
Usadel, Bjoern .
BIOINFORMATICS, 2014, 30 (15) :2114-2120
[5]   Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research [J].
Conesa, A ;
Götz, S ;
García-Gómez, JM ;
Terol, J ;
Talón, M ;
Robles, M .
BIOINFORMATICS, 2005, 21 (18) :3674-3676
[6]   The antioxidant and radical scavenging activities of black pepper (Piper nigrum) seeds [J].
Gülçin, I .
INTERNATIONAL JOURNAL OF FOOD SCIENCES AND NUTRITION, 2005, 56 (07) :491-499
[7]   De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species [J].
Huang, Xiu ;
Yan, Hai-Dong ;
Zhang, Xin-Quan ;
Zhang, Jian ;
Frazier, Taylor P. ;
Huang, De-Jun ;
Lu, Lu ;
Huang, Lin-Kai ;
Liu, Wei ;
Peng, Yan ;
Ma, Xiao ;
Yan, Yan-Hong .
FRONTIERS IN PLANT SCIENCE, 2016, 7
[8]   CAP3: A DNA sequence assembly program [J].
Huang, XQ ;
Madan, A .
GENOME RESEARCH, 1999, 9 (09) :868-877
[9]   Phylogeny and patterns of floral diversity in the genus Piper (Piperaceae) [J].
Jaramillo, MA ;
Manos, PS .
AMERICAN JOURNAL OF BOTANY, 2001, 88 (04) :706-716
[10]   PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants [J].
Jin, Jinpu ;
Tian, Feng ;
Yang, De-Chang ;
Meng, Yu-Qi ;
Kong, Lei ;
Luo, Jingchu ;
Gao, Ge .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D1040-D1045