Based on transcriptome sequencing technology, what is the impact of transcriptome sequencing technology on the biological information of Cinnamomum chinensis?
Foreword: Rhododendron is a general term for Rhododendron in the Rhododendron family, which is widely distributed in China and rich in natural resources. Honeysuckle belongs to the subgenus of honeysuckle model plants in this genus, with a corolla of 1.6~2.3cm, lilac, purple or pink flowers, with fragrance, and horticultural ornamentality.
It is often distributed in the low mountains and hills of eastern China, and is the dominant species in some stands, but it is rarely cultivated in the market, and it is in an undeveloped state, and there is a lack of molecular information.
RNA-Seq (Transcriptome Sequencing Technology) is currently widely used in biological research, with high sensitivity, without the need to know the genetic information of the species, and can directly perform transcriptome analysis of any species, reflecting the transcripts expressed in tissues or cells and the expression level.
In this study, a total of 58.48Gb data were measured in the transcriptome sequencing of the flower samples of Nymphaea chinensis, and the base mass values Q20 and Q30 were 98%~97.72% and 94.38%~93.63%, respectively, indicating that the sequencing quality of Honeysuckle was high and the follow-up analysis results were reliable.
Finally, a total of 72782 single-gene clusters were obtained, with a total length of 93338612 bp, the average length and N50 were 1282 bp and 1951 bp, respectively, and the N50 length was 52.18% higher than the average length, indicating that the assembly effect was good.
The number of single-gene clusters with a length between 200~300 bp was the highest, reaching 11523, and the average GC content was 43.88%.
The NR database had the highest number of annotated single-gene clusters of all databases, while the NT database had the least.
A total of 52409 single-gene clusters were annotated in the NR database, and the homologous sequences of the annotations were mainly from the Chinese kiwifruit of the family Kiwiaceae and the genus Kiwi, which may be due to the lack of basic data of Rhododendron in the Rhododendron family, resulting in the transcriptome single-gene clusters not being aligned to the same family species, but the two species belong to the same order Rhododendron.
According to the GO function annotation, it can be divided into 3 categories and 43 subclasses of cellular components, molecular functions and biological processes, and biological processes are divided into 18 subclasses, including 23291 single-gene clusters, of which 9649 single-gene clusters are involved in cellular processes and 4244 single-gene clusters are involved in metabolic processes.
A total of 29,545 single-gene clusters were involved, including 11 subclasses, mainly including cell membranes, cells and organelles, and the number of single-gene clusters was 12,806, 10,413 and 4,551, accounting for 43.35%, 35.24% and 15.4% of the total, respectively.
A total of 46,052 single-gene clusters were involved in molecular functions, including 14 subclasses, of which 20,568 catalytically active single-gene clusters participated, accounting for 44.66% of the total, and 20,087 single-gene clusters were bound to function, accounting for 43.62% of the total, ranking second.
According to the TF classification statistics of single-gene clusters, it can be divided into 58 categories, containing 2081 single-gene clusters, of which the MYB family contains 225 single-gene clusters, which is the largest family.
MYB transcription factors are involved in many biological functions, widely involved in the growth and development of plant roots, stems, leaves, and flowers, and in response to biological or abiotic stresses, and regulate plant hormones, pigment metabolism, and secondary metabolites.
MYB transcription factors are involved in the phenylpropanoid metabolism pathway, and the synthesis of anthocyanins and flavonoids, the secondary products produced by this pathway, is related to MYB factors.
The mTERF family is the second most abundant, and it plays a regulatory role in mitochondrial gene function, and has research value in mitochondrial function, biological evolution, genetic diagnosis and treatment.
A total of 42437 single-gene clusters were annotated according to the KOG database, which were divided into 25 categories, and the largest number of general functional prediction groups contained 9284 annotated monogene clusters, and the signaling mechanism group was the second most numbered group, containing 5315 annotated single-gene clusters.
From the transcriptome sequencing data of Ma Yinhua, 32261 SSR loci were retrieved, with a frequency of 44.33%, and the highest repetition rate was dinucleotide, accounting for 65.40% of the total, followed by trinucleotides, accounting for 17.01% of the total.
The length of SSR varies between 12~76bp, and the average length of SSR is 22.15bp.
Transcriptome sequencing studies were carried out on the flowers of Nymphauria, and a total of 72782 single gene clusters with N50 of 1951 bp were obtained after data assembly.
N50 is an important index to evaluate the quality of transcriptome assembly, and the length of N50 in this study is 1055 bp for Cyanosis and 1446 bp for Acacia, indicating that the transcriptome assembly sequence quality of Nymphaea japonica is high.
Conclusion:
A total of 32261 SSR loci were retrieved in the single-gene cluster, and the occurrence frequency was 44.33%, which was higher than that of some plants, such as Rhododendron long-stemmed Rhododendron (23.42%), Rhododendron longiflora (27.24%), and P. nanmu (13.97%), which may be related to different plant species, or may be caused by different transcriptome analysis or SSR analysis methods.
The type of motif with the highest repetition rate was dinucleotide, accounting for 65.40% of the total, which was the same as R. yunjin and Rhododendron brocade.
SSR molecular markers have been widely used in molecular biology, and the data obtained in this study can be used to analyze the genetic diversity of honeysuckle, identify hybrids, protect new varieties, and improve the breeding process of new varieties.
