Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages
Abstract
:1. Introduction
2. Results and Discussion
2.1. Generation of the Full-Length Enriched and Normalized cDNA
2.2. Characterization of A. sisalana cDNA Libraries
2.3. Gene Ontology Annotation and Bioinformatics Analysis
2.4. Tissue-Specific Gene Expression
2.4.1. Asknox Expression Characteristics Related to Organogenesis
2.4.2. Expression Characteristics of MADS-Box Gene Family Related to Floral Development
3. Experimental Section
3.1. Plant Materials
3.2. Poly(A+) RNA Isolation and First-Strand cDNA Synthesis
3.3. Amplification of cDNA by Long-Distance Polymerase Chain Reaction
3.4. First-Strand cDNA Normalization and Amplification
3.5. Construction and Quality Analysis of cDNA Library
3.6. Sequence Processing and Analysis
3.7. Gene Expression Analysis by Real-Time PCR
4. Conclusions
Supplementary Materials
ijms-13-13150-s001.pdfAcknowledgments
- Conflict of InterestThe authors declare no conflict of interest.
References
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Description | Number |
---|---|
Total number of successful sequences | 3875 |
Unique sequences | 3320 |
5′ end unigenes | 2080 |
3′ end unigenes | 2402 |
Full-length genes | 1162 |
Number of known genes | 2158 |
Unique unknown genes | 1162 |
Library ID a | Functional annotation b | E-value | Accession No. | Organism species |
---|---|---|---|---|
SF1324 | Knotted1-like homeobox protein | 4 × 10−112 | CAB88029 | Dendrobium nobile |
SL980 | NADP-dependent malic enzyme | 1 × 10−91 | ABR26037 | Oryza sativa |
SL712 | cytochrome P450 like_TBP | 3 × 10−95 | BAA10929 | Nicotiana tabacum |
SL349 | ATP synthase subunit beta | 6 × 10−122 | XP003627732 | Medicago truncatula |
SF1073 | unknown protein | 2 × 10−133 | ACU14517 | Glycine max |
SF1130 | MADS-box transcription factor | 4 × 10−155 | ABC70707 | Asparagus virgatus |
SL453 | chloroplast photosystem | 1 × 10−37 | ACZ54010.1 | Wolffia arrhiza |
SL324 | Sucrose synthase | 8 × 10−104 | XP003591492 | Medicago truncatula |
SS239 | Disease resistance protein | 2 × 10−45 | XP002275269 | Vitis vinifera |
SS136 | UDP-glucosyltransferase | 2 × 10−80 | NP001154307 | Arabidopsis thaliana |
SF201 | Ribulose-1,5-bisphosphate carboxylase | 3 × 10−180 | AFA55129 | Agave schottii |
SS712 | Conserved hypothetical protein | 2 × 10−110 | BAD94036 | Arabidopsis thaliana |
SL506 | Methionyl-tRNA synthetase | 4 × 10−189 | AAC99620 | Oryza sativa |
SF321 | Sugar transporter | 2 × 10−98 | CAA90628 | Arabidopsis thaliana |
SF603 | Poly(A)-binding protein | 4 × 10−110 | CAC01238 | plumbaginifolia |
Gene name | Orthologous gene a | E-value | Max identity | Gene subfamily | Functional role predicted |
---|---|---|---|---|---|
MADS-box1 | NP_564214 (SEPALLATA 3) | 5 × 10−108 | 67% | AGL2 | E function |
MADS-box2 | NP_186880 (SEPALLATA 2) | 1 × 10−82 | 60% | AGL2 | E function |
MADS-box5 | NP_179840 (SVP) | 2 × 10−90 | 61% | STMADS11 | Control of flowering time |
MADS-box6 | NP_191002 (APETALA 3) | 7 × 10−69 | 51% | DEF | Class B floral homeotic gene |
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Zhou, W.-Z.; Zhang, Y.-M.; Lu, J.-Y.; Li, J.-F. Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages. Int. J. Mol. Sci. 2012, 13, 13150-13168. https://doi.org/10.3390/ijms131013150
Zhou W-Z, Zhang Y-M, Lu J-Y, Li J-F. Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages. International Journal of Molecular Sciences. 2012; 13(10):13150-13168. https://doi.org/10.3390/ijms131013150
Chicago/Turabian StyleZhou, Wen-Zhao, Yan-Mei Zhang, Jun-Ying Lu, and Jun-Feng Li. 2012. "Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages" International Journal of Molecular Sciences 13, no. 10: 13150-13168. https://doi.org/10.3390/ijms131013150