**5. Conclusions**

The cluster-based correlation analysis method described in this work, C-CorA, is a new correlation coefficient calculation algorithm. It uses the clustering result from the original data sets to do the correlation analysis. It can deal with various types of data and data in different dimensions. This method was applied to a set of RNA-Seq data of loquat fruit. It identified the fruit lignification correlated structural genes and transcription factors as candidate genes for further research. Using this analysis, we also identified two additional genes (*EjCAD4* and MYB), which were not detected in our previous work, as candidates for involvement in the lignification process. The loquat fruit case indicates that compared to other correlation methods, the C-CorA may be a better choice for fruit quality studies.

**Supplementary Materials:** The following are available online at https://www.mdpi.com/article/ 10.3390/horticulturae8020124/s1: Table S1: genes correlated with the lignin content of loquat fruit during postharvest treatments (0 oC, LTC, HT) from C-CorA, showing their correlation coefficients and annotations; Table S2: genes correlated with the EjCAD4 (UN26767) from C-CorA.; Table S3: genes act synergistically with EjCAD4 on the fruit lignin content identified by C-CorA.

**Author Contributions:** Conception and design: K.C., Q.W., W.L. and W.C. Algorithm design and implementation: W.L. Data analysis and interpretation: J.Q., W.L., W.C., Y.S. and M.Z. Manuscript writing: J.Q. and W.L. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was supported by grants from the National Natural Science Foundation of China (11771393, 11632015 and 31630067) and the Natural Science Foundation of Zhejiang Province, China (LZ14A010002). The funding bodies did not play any role in the design of the study, data collection and analysis or preparation of the manuscript.

**Data Availability Statement:** The raw RNA-Seq data used in this work was submitted to the NCBI Sequence Read Archive (SRA) under the accession SRP128075.

**Acknowledgments:** We thank Don Grierson for helpful suggestions and comments on the manuscript.

**Conflicts of Interest:** The authors declare no conflict of interest.

#### **References**

