Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara
Abstract
:1. Introduction
2. Results
2.1. Sample Collection, Illumina Sequencing, and De Novo Assembly
2.2. Functional Annotation of the Unique Transcripts
2.3. Gene Expression in the Ovaries of GGO and LWL Lantana
2.4. Lantana Gene Families
2.5. Identification and Classification of NBS Genes
2.6. Discovery of Simple Sequence Repeats, Single Nucleotide Polymorphisms, and Insertion or Deletions
3. Discussion
4. Materials and Methods
4.1. Plant Materials, RNA Extraction, and Sequencing
4.2. Sequence Trimming, De Novo Assembly, and Clustering
4.3. Function Annotation
4.4. Mapping and Gene Expression
4.5. Lantana Gene Families Involved in Unreduced Gamete Production, Drought Tolerance, Salt Tolerance, and Allelopathy
4.6. Identification of NBS Genes and Phylogenetic Analysis
4.7. Identification and Annotation of SSR, SNP, and Indel Variants
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Trinity | CD-HIT-EST | TransDecoder (Full-Length) | |
---|---|---|---|
No. of sequences | 112,505 | 90,641 | 29,383 |
Total length (bp) | 126,460,570 | 94,042,530 | 57,219,462 |
Average length (bp) | 1124 | 1037.53 | 1947.40 |
N50 (bp) | 1787 | 1692 | 2206 |
Minimum length (bp) | 201 | 201 | 327 |
Maximum length (bp) | 12,218 | 12,218 | 12,083 |
Biological Process | Gene Ontology (Including Child Terms) | No. of Transcripts |
---|---|---|
Cell cycle | GO:0007049 | 57 |
Regulation of cell cycle | GO:0051726 | 25 |
Positive regulation of cell cycle | GO:0045787 | 16 |
Negative regulation of cell cycle | GO:0045786 | 5 |
Meiotic cell cycle | GO:0051321 | 22 |
Cytokinesis | GO:0000910 | 53 |
Chromosome organization | GO:0051276 | 34 |
Chromosome segregation | GO:0007059 | 18 |
Chromosome organization involved in meiotic cell cycle | GO:0070192 | 16 |
Gamete generation | GO:0007276 | 8 |
Total (unique) | 214 |
NBS Gene Class | Number of Genes |
---|---|
CC-NBS-LRR | 12 |
CC-NBS | 29 |
NBS-LRR | 7 |
NBS | 43 |
Total | 91 |
SSRs | Repeat Motif Length | Total | ||||
---|---|---|---|---|---|---|
Di- | Tri- | Tetra- | Penta- | Hexa- | ||
SSRs identified in transcript assembly | 7886 | 2118 | 101 | 30 | 55 | 10,190 |
SSRs designed with primers | 7325 | 2007 | 97 | 30 | 54 | 9513 |
SNP Type | SNP Number | INDEL Number | GGO Genotype | LWL Genotype |
---|---|---|---|---|
Homozygous | 11,865 | 1014 | 0/0 | 1/1 |
13,115 | 1070 | 1/1 | 0/0 | |
Heterozygous | 54,628 | 3052 | 0/0 | 0/1 |
74,210 | 4194 | 0/1 | 0/0 | |
6494 | 377 | 0/1 | 1/1 | |
4917 | 277 | 1/1 | 0/1 | |
Total | 165,229 | 9984 |
Variant Effects | Count | Percentage (%) | Variant Type |
---|---|---|---|
Synonymous variant | 51,878 | 33.67 | SNP |
Missense variant | 45,326 | 29.42 | SNP |
3′ UTR variant | 31,145 | 20.22 | SNP |
5′ UTR variant | 21,390 | 13.88 | SNP |
5′ UTR premature start codon gain variant | 3568 | 2.32 | SNP |
Stop gained | 529 | 0.34 | SNP |
Stop lost | 119 | 0.08 | SNP |
Stop retained variant | 62 | 0.04 | SNP |
Start lost | 42 | 0.03 | SNP |
Initiator codon variant | 9 | 0.01 | SNP |
3′ UTR variant | 3497 | 39.34 | Indel |
5′ UTR variant | 2720 | 30.60 | Indel |
Frameshift variant | 1029 | 11.58 | Indel |
Conservative inframe deletion | 516 | 5.80 | Indel |
Conservative inframe insertion | 471 | 5.30 | Indel |
Disruptive inframe deletion | 309 | 3.48 | Indel |
Disruptive inframe insertion | 245 | 2.76 | Indel |
Stop gained | 49 | 0.55 | Indel |
Stop lost | 30 | 0.34 | Indel |
Start lost | 23 | 0.26 | Indel |
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Peng, Z.; Bhattarai, K.; Parajuli, S.; Cao, Z.; Deng, Z. Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara. Plants 2019, 8, 263. https://doi.org/10.3390/plants8080263
Peng Z, Bhattarai K, Parajuli S, Cao Z, Deng Z. Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara. Plants. 2019; 8(8):263. https://doi.org/10.3390/plants8080263
Chicago/Turabian StylePeng, Ze, Krishna Bhattarai, Saroj Parajuli, Zhe Cao, and Zhanao Deng. 2019. "Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara" Plants 8, no. 8: 263. https://doi.org/10.3390/plants8080263
APA StylePeng, Z., Bhattarai, K., Parajuli, S., Cao, Z., & Deng, Z. (2019). Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara. Plants, 8(8), 263. https://doi.org/10.3390/plants8080263