The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user‐friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication‐quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch‐site, and clade models of selection. The program allows comparison of major codon‐based models for analyses of selection. EasyCodeML is a stand‐alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML .

In natural conditions, it takes more than 3 years to complete the Ananas juvenile phase, and another 2 years for adult vegetative growth of the plantlet from in vitro buds. Ethylene has often been used to shorten the juvenile and vegetative phases to produce earlier flowering. It is important to induce in vitro flowering of Ananas plants to understand the flowering mechanism more completely, which is also related to flower organ differentiation and development as well as the pineapple fruit eye development. In this study, Murashige and Skoog (MS) basal medium was used to select the best combination for adventitious bud induction from the callus of Ananas bracteatus var. tricolor (A. tricolor). Flower induction from the callus was studied using 6-benzyladenine (6-BA) and 1-naphthylacetic acid (NAA) at four different concentrations (0, 1.0, 2.0, and 3.0 mg⋅L–1). Our results showed that when MS was added with 3 mg⋅L–1 6-BA and 2 mg⋅L–1 NAA under 2000 μmol⋅m–2⋅s–1 of light for 16 hours per day at a temperature of 20 °C, the callus of A. tricolor grew quickly, and adventitious buds were induced. After more than four successive subcultures (at day 80), differentiation of flower buds was observed on the aging callus tissue before a complete floral organ developed. This research could be used for the flowering regulation of Ananas plants in the future. Inducing flowers directly from the callus has important scientific significance for the differentiation and morphogenesis of Ananas plants.

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Background: Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In this study, green and red parts of chimeric leaves of Ananas comosus var. bracteatus were sampled and anthocyanin accumulation differences were comparatively analyzed at phenotypic, cellular and molecular levels.Results: A CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including MYB5 and MYB82, were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95. Conclusion: Phenotypic colors are closely related to the tissue structures of different leaf parts of Ananas comosus var. bracteatus, and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of Ananas comosus var. bracteatus chimeric leaves. This study lay a foundation for further researches on functions of MYBs in Ananas comosus var. bracteatus and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.