AP2/ERF (APETALA2/Ethylene Responsive Factor) transcription factors, a class of plant-specific transcription factors, play a pivotal role in plant growth, development, metabolism, and stress response. The pineapple (Ananas comosus (L.) Merr.), a perennial fruit, belongs to the Bromeliaceae family. It is an economically important crop worldwide, which is consumed as fresh fruit, canned fruit, a fiber source, and even pharmaceutical raw material. We identified 75 AcoAP2/ERF genes in the pineapple genome, with four manually curated. They were distributed evenly on 23 chromosomes, except on LG20 and LG23. Sequence lengths, molecular weights, and intron numbers were diverse. The majority of pineapple AcoAP2/ERF genes were localized in nuclear while seven AcoERFs were located in mitochondrial or chloroplast. All pineapple AcoAP2/ERF genes possess an AP2 domain and are divided into 10 clades. Most originate from whole-genome or segmental duplication instead of transposon events. Utilizing pineapple calluses as experimental material, qRT–PCR analysis revealed that the expression of the majority of AcoAP2/ERF genes was induced in response to abscisic acid (ABA), gibberellic acid (GA), ethylene (ET), and naphthalene acetic acid (NAA). In this study, we cloned the promoter sequence of the AcoERF24 gene and divided it into three fragments to construct individual vectors. These vectors were subsequently introduced into Arabidopsis thaliana for β-glucuronidase (GUS) activity analysis, revealing variations in activity levels among the different fragments. This study not only deepens our understanding of the AcoAP2/ERF genes family in olives but also provides an important basis for subsequent studies on the regulation of AcoERF24 gene expression and biological functions.

Ananas comosus var. bracteatus, known for its ornamental chimeric leaves, exhibits a colorful pattern due to a combination of central photosynthetic tissue (CP) and marginal albino tissue (MA). The leaves turn red during spring and autumn, driven by changes in pigments biosynthesis. This study explored the role of AbPIF3, a key regulator, in controlling pigments biosynthesis in chimeric leaves. The albino phenotype in MA resulted from reduced chlorophyll and carotenoid content, while the red coloration was due to anthocyanin accumulation, which was significantly higher in MA than CP. The expression of AbPIF3 correlated positively with anthocyanin content and was higher in MA than CP. AbPIF3 promoted the transcription of AbCHS (involved in anthocyanin synthesis) while suppressing AbPSY (related to carotenoid synthesis). Exogenous ABA and dark treatments enhanced AbPIF3 transcription, whereas light reduced it. Over expression of AbPIF3 leaded to reduced expression levels of NbDVR and NbPSY and increased NbCHS, thereby decreasing chlorophyll and carotenoid content while increasing anthocyanin content. The study revealed how AbPIF3 regulated the balance of pigments accumulation in the CP and MA regions, providing insights into the mechanisms underlying chimeric leaf color formation and pigments biosynthesis in A. comosus var. bracteatus.

Sepals and petals form the peels of pineapple fruits, which influence the size of cavities below the surface of the fruits (so-called “fruit eye”) and subsequently the fruit quality and edible rate. In this study, to investigate the underlying mechanisms controlling septal-petal formation in pineapple, we utilized a mutant of variety ‘Yulinglong’ with petaloid sepals for comparative analyses with the wild type. Phenotypic and microscopic observations confirmed the either partially or completely petalized structure of the sepals of the mutant. Comparative gene expression analysis identified two MADS-box family members AcPI and AcAP3 that are potentially associated with the petaloid sepals. Heterologous overexpression experiments in Arabidopsis and tobacco validated their functions in controlling the identity and organogenesis of sepals/petals, as well as confirmed their role in transforming sepals to petals. Protein-protein interaction experiments and gene expression profiling suggested that AcPI and AcAP3 may coordinately determine floral organogenesis in pineapple flower bud primordia differentiation. The results provide important insights into the molecular regulation of floral organ identity and peel structure formation in pineapple, which may be harnessed to improve fruit quality and edible rate for pineapple.

Sucrose transporter (SUT) plays essential roles in plant growth and development, as well as responses to diverse abiotic stresses. However, limited information about the function of SUT was available in pineapple, an important tropical fruit crop with crassulacean acid metabolism. Here, four AcSUT genes were identified in pineapple genome, and divided into three clades according to the phylogenetic analysis. The expression profiles of AcSUTs were systemically examined, and they were all localized to plasma membrane. Transport activity assay by two-electrode voltage clamp of Xenopus oocytes showed that AcSUT1A and AcSUT1B were capable of transporting a range of glucosides, and they were exhibited high affinity for sucrose with Km value of 0.09 mM and 0.41 mM at pH 5.0, respectively. Overexpression of the cold-induced AcSUT1B conferred enhanced cold tolerance in transgenic Arabidopsis. DNA-protein interaction analysis further demonstrated that AcCBF1 directly binds the CRT/DRE element of the AcSUT1B promoter and activated its expression. Heterologous expression of AcCBF1 in Arabidopsis also increased cold tolerance. In this study, we investigated the transport activities of AcSUTs in pineapple and identified the AcCBF1-AcSUT1B module involved in cold stress, which provided new insights into the molecular mechanism of the cold response in pineapple.

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. In this study, we sequenced the genomes of three varieties: a wild pineapple variety, a fiber pineapple variety, and a globally cultivated edible pineapple variety. We constructed the first gap-free reference genome (Ref) for pineapple. By consolidating multiple sources of evidence and manually revising each gene structure annotation, we identified 26,656 protein-coding genes. The BUSCO evaluation indicated a completeness of 99.2%, demonstrating the high quality of the gene structure annotations in this genome. Utilizing these resources, we identified 7,209 structural variations across the three varieties. Approximately 30.8% of pineapple genes were located within ±5 kb of structural variations, including 30 genes associated with anthocyanin synthesis. Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves, both of which may be affected by a 1.9-kb insertion fragment. In addition, we developed the Ananas Genome Database, which offers data browsing, retrieval, analysis, and download functions. The construction of this database addresses the lack of pineapple genome resource databases. In summary, we acquired a seamless pineapple reference genome with high-quality gene structure annotations, providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.

Red fruit peel is an attractive target for pineapple breeding. Various pineapple accessions with distinct red coloration patterns exist; however, the precise molecular mechanism accounting for these differences remains unknown, which hinders the pineapple breeding process from combining high fruit quality with red peel. In this study, we characterized a transcription factor, AcMYB266, which is preferentially expressed in pineapple peel and positively regulates anthocyanin accumulation. Transgenic pineapple, Arabidopsis, and tobacco plants overexpressing AcMYB266 exhibited significant anthocyanin accumulation. Conversely, transient silencing of this gene led to decreased anthocyanin accumulation in pineapple red bracts. In-depth analysis indicated that variations of AcMYB266 sequences in the promoter instead of the protein-coding region seem to contribute to different red coloration patterns in peels of three representative pineapple varieties. In addition, we found that AcMYB266 was located in a cluster of four MYB genes exclusive to and conserved in Ananas species. Of this cluster, each was proved to regulate anthocyanin synthesis in different pineapple tissues, illustrating an interesting case of gene subfunctionalization after tandem duplication. In summary, we have characterized AcMYB266 as a key regulator of pineapple red fruit peel and identified an MYB cluster whose members were subfunctionalized to specifically regulate the red coloration of different pineapple tissues. The present study will assist in establishing a theoretical mechanism for pineapple breeding for red fruit peel and provide an interesting case for the investigation of gene subfunctionalization in plants.

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. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, bracts, flowers, and peels makes it an important plant with a long ornamental period and highly improves its commercial value. We conducted a comprehensive bioinformatic analysis of the R2R3-MYB gene family based on genome data from A. comosus var. bracteatus. Phylogenetic analysis, gene structure and motif analysis, gene duplication, collinearity, and promoter analysis were used to analyze the characteristics of this gene family. In this work, a total of 99 R2R3-MYB genes were identified and classified into 33 subfamilies according to phylogenetic analysis, and most of them were localized in the nucleus. We found these genes were mapped to 25 chromosomes. Gene structure and protein motifs were conserved among AbR2R3-MYB genes, especially within the same subfamily. Collinearity analysis revealed four pairs of tandem duplicated genes and 32 segmental duplicates in AbR2R3-MYB genes, indicating that segmental duplication contributed to the amplification of the AbR2R3-MYB gene family. A total of 273 ABRE responsiveness, 66 TCA elements, 97 CGTCA motifs, and TGACG motifs were the main cis elements in the promoter region under response to ABA, SA, and MEJA. These results revealed the potential function of AbR2R3-MYB genes in response to hormone stress. Ten R2R3-MYBs were found to have high homology to MYB proteins reported to be involved in anthocyanin biosynthesis from other plants. RT-qPCR results revealed the 10 AbR2R3-MYB genes showed tissue-specific expression patterns, six of them expressed the highest in the flower, two genes in the bract, and two genes in the leaf. These results suggested that these genes may be the candidates that regulate anthocyanin biosynthesis of A. comosus var. bracteatus in the flower, leaf, and bract, respectively. In addition, the expressions of these 10 AbR2R3-MYB genes were differentially induced by ABA, MEJA, and SA, implying that these genes may play crucial roles in hormone-induced anthocyanin biosynthesis. Our study provided a comprehensive and systematic analysis of AbR2R3-MYB genes and identified the AbR2R3-MYB genes regulating the spatial-temporal anthocyanin biosynthesis in A. comosus var. bracteatus, which would be valuable for further study on the anthocyanin regulation mechanism of A. comosus var. bracteatus.

Background:Pineapple is the only commercially grown fruit crop in the Bromeliaceae family and has significant agricultural, industrial, economic, and ornamental value. GRF (growth-regulating factor) proteins are important transcription factors that have evolved in seed plants (embryophytes). They contain two conserved domains, QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys), and regulate multiple aspects of plant growth and stress response, including floral organ development, leaf growth, and hormone responses. The GRF family has been characterized in a number of plant species, but little is known about this family in pineapple and other bromeliads. Main discoveries:We identified eight GRF transcription factor genes in pineapple, and phylogenetic analysis placed them into five subfamilies (I, III, IV, V, VI). Segmental duplication appeared to be the major contributor to expansion of the AcGRF family, and the family has undergone strong purifying selection during evolution. Relative to that of other gene families, the gene structure of the GRF family showed less conservation. Analysis of promoter cis-elements suggested that AcGRF genes are widely involved in plant growth and development. Transcriptome data and qRT-PCR results showed that, with the exception of AcGRF5, the AcGRFs were preferentially expressed in the early stage of floral organ development and AcGRF2 was strongly expressed in ovules. Gibberellin treatment significantly induced AcGRF7/8 expression, suggesting that these two genes may be involved in the molecular regulatory pathway by which gibberellin promotes pineapple fruit expansion. Conclusion:AcGRF proteins appear to play a role in the regulation of floral organ development and the response to gibberellin. The information reported here provides a foundation for further study of the functions of AcGRF genes and the traits they regulate.

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. In this upgrade, we have incorporated over 100 new features, such as those for comparative genomics analysis, phylogenetic analysis, and data visualization. Meanwhile, to better meet the increasing needs of personalized data analysis, we have launched the plugin mode, which enables users to develop their own plugins and manage their selection, installation, and removal according to individual needs. To date, the plugin store has amassed over 50 plugins, with more than half of them being independently developed and contributed by TBtools users. These plugins offer a range of data analysis options including co-expression network analysis, single-cell data analysis, and bulked segregant analysis sequencing data analysis. Overall, TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors. By promoting the theme "one for all, all for one", we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.

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 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants.

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 Prunus salicina 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. Compared to normal seedlings, the photosynthetic pigment contents in albino seedlings decreased by more than 90%, accompanied by significant reductions in several chlorophyll fluorescence parameters. Furthermore, substantially changed photosynthetic parameters indicated that the photosynthetic capacity and stomatal function were impaired in albino seedlings. Additionally, the activities of the antioxidant enzyme were drastically altered against the background of higher proline and lower ascorbic acid in leaves of albino seedlings. A total of 4048 differentially expressed genes (DEGs) were identified through transcriptomic sequencing, and the downregulated DEGs in albino seedlings were greatly enriched in the pathways for photosynthetic antenna proteins and flavonoid biosynthesis. GLK1 and Ftsz were identified as candidate genes responsible for the impaired chloroplast development and division in albino seedlings. Additionally, the substantial decline in the expression levels of examined photosystem-related chloroplast genes was validated in albino seedlings. Our findings shed light on the intricate physiological and molecular mechanisms driving albino plum seedling manifestation, which will contribute to improving the reproductive and breeding efforts of plums.

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 findings suggest that the changes in the expression of key structural genes (early and late biosynthetic genes) of the anthocyanin (cyanidin) biosynthesis pathway are responsible for peel discoloration. Based on a gene co-expression analysis and a transient expression, two transcription factors i.e., AcHOX21 and AcMYB12, were identified, whose’ downregulation leads to reduced anthocyanin accumulation with fruit maturation. The endogenous levels of jasmonic acid, gibberellic acid, and auxins are also involved in anthocyanin-content-led peel discoloration. Overall, the discovery of genes regulating anthocyanin biosynthesis in pineapple peel provides a theoretical basis for improving the fruit’s aesthetic value through genetic engineering.

Somatic embryogenesis (SE) is a key regeneration process in plant. AcSERK1 is a gene specifically expressed in the early stage of SE in pineapple ( Ananas comosus ), suggesting that the promoter of SERK1 might contain specific cis-acting element regulating SE. To identify embryonic cell-specific element in the SERK1 promoter, a series of binary plant transformation vectors with GUS (β-glucuronidase) reporter gene were systematically analyzed by transient gene expression system in wild-type and transgenic pineapple embryogenic callus. Histochemical and quantitative GUS assays demonstrated that the activity of the AcSERK1 upstream regulatory sequence lacking − 921 to -911 or -910 to -880 was significantly reduced in the embryonic callus of the pineapple, and these two regions were needed for the embryonic cell-specific. Besides, a promoter lacking − 943 to -922 was shown to significantly increase GUS activity in embryogenic callus, suggesting repressive elements exist in this region. Our data of stable transformation assays confirmed again the 5’ upstream regulatory sequence (-921 to -880) of the AcSERK1 gene is an essential functional region. Our findings lay the basis for better understanding of the molecular mechanisms of AcSERK1 gene in the regulation in early stage of SE.

In recent years, transgenic technology has become the most important tool for molecular breeding. An efficient genetic transformation system is the key to improving the efficiency of biological breeding, and Agrobacterium-mediated genetic transformation is the common method used in plant genetic transformation experiments. Pineapple is an important tropical horticultural plant, but it has a very narrow genetic base, high genome heterozygosity, and strict self-incompatibility, thus limiting the value of conventional breeding techniques. To shorten the breeding cycle and create new subversive varieties, transgenic research of pineapple is imperative. Due to the characteristics of pineapple, in vitro regeneration technology is relatively straightforward, but it can still be very difficult to obtain pineapple transgenic materials. Over more than 20 years of research on pineapple genetic transformation, we have explored, continuously improved and now established a set of transformation tools for the simple and effective transformation of pineapple genes. The basic premise of our approach is a straightforward redifferentiation of pineapple suckers as explants. Specifically, the receptor material that is the basis for the successful transformation of pineapple is the in vitro culture of callus, which is a tissue that has not yet entered the organ differentiation stage. The nptII gene was selected as the optimal selection marker gene and the somatic embryogenesis pathway is used for screening and regeneration.

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.

Abstract Background: growth-regulating factors（GRFs）are plant-specific transcription factors that play an important role in plant growth and development, Although the GRF gene family has been identified in many species, a genome-wide analysis of this gene family in pineapple has not been reported.Results: In this study, 8 pineapple GRF genes (AcGRF) were identified and renamed according to their chromosomal locations.8 AcGRFs were divided into three main families and subgroups based on their structural and phylogenetic characteristics. Genomic collinearity analysis found that segmental duplication played a more important role in the expansion of the pineapple GRF gene family. GRF gene collinearity analysis and phylogenetic analysis provide deeper insights into the evolutionary characteristics of pineapple GRF genes. Transcriptome data and real-time quantitative PCR analysis revealed AcGRF gene expression patterns in various tissues and responses to different abiotic stresses and hormonal treatments.Conclusions: In this study, 8 GRF genes were identified in pineapple, and their coding gene structures, evolutionary characteristics, and expression patterns were analyzed. This systematic analysis provides a basis for further identification of pineapple GRF gene function.

Ananas comosus var. erectifolius (L.B. Smith) Coppens & Leal, a tropical plant from Bromeliaceae family, has immense applications, especially for fiber production of excellent quality. The lack of available chloroplast (cp) genome information limits its breeding and application. Here, we assembled its complete cp genome using Illumina high-throughput sequencing technology. The cp genome size is 159,983 bp, with 37.4% GC content, including a large single copy region (LSC) of 87,787 bp, a small single copy region (SSC) of 18,606 bp, and a pair of inverted repeat regions (IRs) of 26,795 bp. It encodes 89 protein-coding, 38 tRNA and 8 rRNA genes. Phylogenetic analysis showed that A. comosus var. erectifolius was close to Ananas comosus. The complete cp genome sequences could provide valuable information for variety breeding and genetic analysis of agronomic and economic traits in A. comosus var. erectifolius.

Cold stress is an important factor limiting the growth and distribution of pineapple. Breeding cold-resistant germplasm is an effective way to cope with this problem. In vitro selection for the somaclonal variation using different selection agents has been used for crop improvement in stress tolerance. In this study, the pineapple cold-tolerant variant was developed through in vitro cold selection of somaclonal variations. Low temperature was used as the selected agent, and the extreme lethal condition for the in vitro pineapple cultures was determined to be 0 °C for 72 h. The morphology changes of the in vitro cultures during the cold selection were observed and analyzed. The cold-tolerant variant line was finally obtained through three consecutive selections with cold shock treatments, based on the established high-efficiency culture system for pineapple embryogenic calli. The genetic variations at the molecular level in the cold-tolerant variant were verified by ISSR analysis. The significantly improved cold tolerance in our selected variant was mainly reflected by the higher survival rate, increased proline content, and elevated SOD activity under cold stress compared to these qualities in the control plants. This study demonstrated the feasibility of in vitro selection for cold tolerance in pineapple. The cold-tolerant variant could be valuable for future pineapple breeding programs and for cold tolerance research.

以不同菠萝种质的顶芽、花和果实为材料,通过组织切片和解剖观察果眼形成过程,测定和分析果眼相关组织器官的动态变化.菠萝果眼形成过程分为花腔分化、花腔发育和果眼发育3个阶段.花腔是果眼的早期形态,其分化和发育过程约需70 d;而坐果标志着果眼发育阶段的起始.花腔形态分化是从花萼分化开始,至花盘(含花托和子房)分化结束;催花后14d顶芽基部首先出现花萼原基分化,自下而上,35 d时花腔分化结束,花序顶部花腔形态分化完成时间比基部迟7d左右.形态分化完成后进入花腔发育阶段,催花36～42 d是花腔膨大高峰期,此时深、浅果眼品种的花腔深度开始出现显著差异,此后膨大逐渐减缓;品种间花盘的绝对生长量相差不大,花腔的加深主要取决于花萼的生长.坐果后进入果眼发育期,随着果实迅速膨大,萼筒背腹面生长不均衡,宿萼向内弯曲;但宿萼弯曲速度和生长停止时间因品种而异,浅果眼品种'MD-2'宿萼伸长生长量小、内弯迅速,深果眼品种'金筒'宿萼则生长量较大、内弯缓慢.果眼加深主要在坐果后14d内,坐果约70 d时果眼的形态和大小已不再变化.根据成熟果实中部果眼的深浅,可将菠萝种质划分为浅(果眼深＜ 0.9 cm)、中(果眼深0.9～1.2 cm)、深(果眼深＞ 1.2 cm)3个类型;不同类型品种间花盘深度没有明显差异(约0.29 cm),果眼深浅差异主要由宿萼高度的不同引起,而宿萼的弯曲程度和生长量是导致类型间宿萼高度及小果凸出度出现差异的主要原因.因此,菠萝果眼形成始于花芽分化,花萼生长发育对果眼的形态和深浅产生重大影响,品种间果眼形态差异主要由坐果14 d内萼筒部背腹面生长量不均衡引起,而果眼深浅差异主要发生在花萼发育的前7d(催花36 ～ 42 d).

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. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.