The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis.

Pineapple is the third most crucial tropical fruit worldwide and available in five varieties. Genomes of different pineapple varieties have been released to date; however, none of them are complete, with all exhibiting substantial gaps and representing only two of the five pineapple varieties. This significantly hinders the advancement of pineapple breeding efforts.

Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple ().

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree.

Integrated Cytological, Physiological, and Transcriptome Analyses Provide Insight into the Albino Phenotype of Chinese Plum ().

Albino seedlings that arise during seed reproduction can have a significant impact on plant growth and breeding. In this research, we present the first report of albino occurrences in the seed reproduction process of and describe the cytological, physiological, and transcriptomic changes observed in albino seedlings. The albino seedlings which were observed in several plum cultivars exhibited abnormal chloroplast ultrastructure and perturbed stomatal structure.

TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining.

Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles. Now, TBtools is a commonly used tool in biological laboratories. Over the past 3 years, thanks to invaluable feedback and suggestions from numerous users, we have optimized and expanded the functionality of the toolkit, leading to the development of an upgraded version-TBtools-II.

Genome-Wide Identification and Characterization of Provide Insight into Anthocyanin Biosynthesis Regulation Mechanism of var. .

The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. var. is an important colorful anthocyanins-rich garden plant.

Unveiling the molecular mechanism involving anthocyanins in pineapple peel discoloration during fruit maturation.

Peel color is a key factor that affects the fruit's aesthetic and economic values. Limited knowledge is available on the regulation of pineapple peel discoloration. Here, we report that a decrease in anthocyanin biosynthesis, particularly cyanidin, is predominantly associated with the pineapple peel color change during maturation.

The complete chloroplast genome of var. (L.B. Smith) Coppens & Leal.

var. (L.B.

The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color.

Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering.

Validation of Reference Genes for Quantitative Real-Time PCR Normalization in var. During Chimeric Leaf Development and Response to Hormone Stimuli.

Reverse transcription quantitative real-time PCR (RT-qPCR) is a common way to study gene regulation at the transcriptional level due to its sensibility and specificity, but it needs appropriate reference genes to normalize data, with white-green chimeric leaves, is an important pantropical ornamental plant. Up to date, no reference genes have been evaluated in var. .

Comparative transcriptome analysis of a fan-shaped inflorescence in pineapple using RNA-seq.

Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was exceptionally evolved in pineapple, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between the fan-shaped inflorescence and the wild-shaped inflorescence pineapples were analyzed in three tissues, i.

Adventitious root primordia formation and development in the stem of var. slip.

There are about 4-6 slips on a fruit, and they are good materials for effective regeneration of var. . Adventitious root (AR) induction is essential for the propagation of slips.

Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus.

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.

encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino var. leaves.

Background: The chimeric leaves of var. are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in var.

Chromosome-level draft genome of a diploid plum (Prunus salicina).

Background: Plums are one of the most economically important Rosaceae fruit crops and comprise dozens of species distributed across the world. Until now, only limited genomic information has been available for the genetic studies and breeding programs of plums. Prunus salicina, an important diploid plum species, plays a predominant role in modern commercial plum production.

Genome-wide identification and expression analysis of the MYB transcription factor in Japanese plum (Prunus salicina).

MYB proteins constitute one of the largest transcription factor families in plants, members of which are involved in various plant physiological and biochemical processes. Japanese plum (Prunus salicina) is one of the important stone fruit crops worldwide. To date, no comprehensive study of the MYB family in Japanese plum has been reported.

Transcriptional analysis for the difference in carotenoids accumulation in flesh and peel of white-fleshed loquat fruit.

Loquat (Eriobotrya japonica Lindl.) is divided into yellow- and white-fleshed based on the difference in fruit color, and the variations in carotenoids accumulation are considered as the main reasons for this difference. Using RNA-seq technology, a transcriptome analysis was carried out on the flesh and peel of 'Baiyu' fruit during four different fruit development stages.

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface.

Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus.

Background: Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var.

Identification of key taste components in loquat using widely targeted metabolomics.

Loquats can be divided into white- and yellow-fleshed cultivars. Generally, white-fleshed cultivars taste better than yellow-fleshed cultivars. Currently, metabolic causes of differences in taste are unknown, due to the lack of a large-scale and comprehensive investigation of metabolites in loquat fruit.

Methylation Analysis of CpG Islands in Pineapple Promoter.

Somatic embryogenesis (SE) is a more rapid and controllable method for plant propagation than traditional breeding methods. However, it often suffers from limited efficiency. promotes SE in several plants, including pineapple ( L.

Screening and characterization of long noncoding RNAs involved in the albinism of Ananas comosus var. bracteatus leaves.

Long noncoding RNAs (lncRNAs) have been reported to play key regulatory roles in plant growth, development, and biotic and abiotic stress physiology. Revealing the mechanism of lncRNA regulation in the albino portions of leaves is important for understanding the development of chimeric leaves in Ananas comosus var. bracteatus.

Identification of an Embryonic Cell-Specific Region within the Pineapple Promoter.

Plant tissue culture methods, such as somatic embryogenesis, are attractive alternatives to traditional breeding methods for plant propagation. However, they often suffer from limited efficiency. Somatic embryogenesis receptor kinase ( is a marker gene of early somatic embryogenesis in several plants, including pineapple.