Analysis of global gene expression profiles during the flowering initiation process of Lilium × formolongi.

The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70.10%) were differentially expressed. The global expression dynamics of the differentially expressed genes were predominant in flowering induction phase I and the floral differentiation stage, but down-regulated in flowering induction phase II. Various transcription factor families relevant to flowering were elucidated, and the members of the MADS-box, SBP and CO-like transcription factor families were the most represented. There were 85 differentially expressed genes relevant to flowering. CONSTANS-LIKE, FLOWERING LOCUS T, TREHALOSE-6-PHOSPHATE SYNTHASE and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE homologs were discovered and may play significant roles in the flowering induction and transition process of L. × formolongi. A putative gene regulatory network, including photoperiod, age-dependent and trehalose-6-phosphate flowering pathways, was constructed. This is the first expression dataset obtained from a transcriptome analysis of photoperiod-mediated flowering pathway in lily, and it is valuable for the exploration of the molecular mechanisms of flowering initiation and the short vegetative stage of L. × formolongi.

De novo transcriptome characterization of Lilium 'Sorbonne' and key enzymes related to the flavonoid biosynthesis.

Lily is an important cut-flower and bulb crop in the commercial market. Here, transcriptome profiling of Lilium 'Sorbonne' was conducted through de novo sequencing based on Illumina platform. This research aims at revealing basic information and data that can be used for applied purposes especially the molecular regulatory information on flower color formation in lily. In total, 36,920,680 short reads which corresponded to 3.32 GB of total nucleotides, were produced through transcriptome sequencing. These reads were assembled into 39,636 Unigenes, of which 30,986 were annotated in Nr, Nt, Swiss-Prot, KEGG, COG, GO databases. Based on the three public protein databases, a total of 32,601 coding sequences were obtained. Meanwhile, 19,242 Unigenes were assigned to 128 KEGG pathways. Those with the greatest representation by unique sequences were for ''metabolic pathways'' (5,406 counts, 28.09 %). Our transcriptome revealed 156 Unigenes that encode key enzymes in the flavonoid biosynthesis pathway including CHS, CHI, F3H, FLS, DFR, etc. MISA software identified 2,762 simple sequence repeats, from which 1,975 primers pairs were designed. Over 2,762 motifs were identified, of which the most frequent was AG/CT (659, 23.86 %), followed by A/T (615, 22.27 %) and CCG/CGG (416, 15.06 %). Based on the results, we believe that the color formation of the Lilium 'Sorbonne' flower was mainly controlled by the flavonoid biosynthesis pathway. Additionally, this research provides initial genetic resources that will be valuable to the lily community for other molecular biology research, and the SSRs will facilitate marker-assisted selection in lily breeding.

Squamous cell carcinoma of ear and temporal bone: A retrospective study on clinicopathological predictors.

BACKGROUND: Ear and temporal bone squamous cell carcinoma (ETBSCC) is a rare and aggressive malignant tumor with minimal clinicopathological studies. The object of this study was to retrospectively evaluate the predictive effect of clinicopathological variables on the 5-year overall survival (OS) rate of ETBSCC patients in a single tertiary medical center in Tianjin, China. METHODS: A cohort of 44 patients with diagnosed ETBSCC from December 2012 to August 2022 were retrospectively studied. Univariate and multivariate analysis were, respectively, performed for the assessment of clinicopathological predictors, including sex, age, history of chronic suppurative otitis media (CSOM), lesion side, diameter, the choice of surgical approach, parotidectomy, neck dissection, adjuvant therapies, T stage, lymph node metastasis, tumor grade, margin, perineural invasion (PNI), and Ki-67 index. RESULTS: Seventeen females and 27 males were included, with the mean age of 65 years old, ranging from 36 to 89 years. The 5-year OS rate was 43% (mean 51 months, 95% confidence interval [CI] = 39-64). Significant prediction of a worse prognosis for 5-year OS rate was observed under univariate analysis for advanced T stage, positive margin, identified PNI, and higher Ki-67 index, respectively. Advanced T stage was confirmed to be an independent prognostic factor strongly affecting 5-year OS rate among this cohort of patients using a multivariate cox proportional hazard model. CONCLUSION: We found that clinicopathological parameters, especially postoperative pathological parameters, play a critical role in predicting the prognosis of ETBSCC patients.

How do plants make mitochondria?

Plant mitochondria can differ in size, shape, number and protein content across different tissue types and over development. These differences are a result of signaling and regulatory processes that ensure mitochondrial function is tuned in a cell-specific manner to support proper plant growth and development. In the last decade, the processes involved in mitochondrial biogenesis are becoming clearer, including; how dormant seeds transition from empty promitochondria to fully functional mitochondria with extensive cristae structures and various biochemical activities, the regulation of nuclear genes encoding mitochondrial proteins via regulators of the diurnal cycle in plants, the mitochondrial stress response, the targeting of proteins to mitochondria and other organelles and connections between the respiratory chain and protein import complexes. All these findings indicate that mitochondrial function is a part of an integrated cellular network, and communication between mitochondria and other cellular processes extends beyond the known exchange or transport of metabolites. Our current knowledge now needs to be used to gain more insight into the molecular components at various levels of this hierarchical and complex regulatory and communication network, so that mitochondrial function can be predicted and modified in a rational manner.

Enhanced store-operated Ca²+ entry and TRPC channel expression in pulmonary arteries of monocrotaline-induced pulmonary hypertensive rats.

Pulmonary hypertension (PH) is associated with profound vascular remodeling and alterations in Ca(2+) homeostasis in pulmonary arterial smooth muscle cells (PASMCs). Previous studies show that canonical transient receptor potential (TRPC) genes are upregulated and store-operated Ca(2+) entry (SOCE) is augmented in PASMCs of chronic hypoxic rats and patients of pulmonary arterial hypertension (PAH). Here we further examine the involvement of TRPC and SOCE in PH with a widely used rat model of monocrotaline (MCT)-induced PAH. Rats developed severe PAH, right ventricular hypertrophy, and significant increase in store-operated TRPC1 and TRPC4 mRNA and protein in endothelium-denuded pulmonary arteries (PAs) 3 wk after MCT injection. Contraction of PA and Ca(2+) influx in PASMC evoked by store depletion using cyclopiazonic acid (CPA) were enhanced dramatically, consistent with augmented SOCE in the MCT-treated group. The time course of increase in CPA-induced contraction corresponded to that of TRPC1 expression. Endothelin-1 (ET-1)-induced vasoconstriction was also potentiated in PAs of MCT-treated rats. The response was partially inhibited by SOCE blockers, including Gd(3+), La(3+), and SKF-96365, as well as the general TRPC inhibitor BTP-2, suggesting that TRPC-dependent SOCE was involved. Moreover, the ET-1-induced contraction and Ca(2+) response in the MCT group were more susceptible to the inhibition caused by the various SOCE blockers. Hence, our study shows that MCT-induced PAH is associated with increased TRPC expression and SOCE, which are involved in the enhanced vascular reactivity to ET-1, and support the hypothesis that TRPC-dependent SOCE is an important pathway for the development of PH.

Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops.

The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.

[TRPC6 mediates the enhancements of pulmonary arterial tone and intracellular Ca2+ concentration of pulmonary arterial smooth muscle cells in pulmonary hypertension rats].

Pulmonary arterial hypertension is associated with profound vascular remodeling and alterations in Ca2+ homeostasis in pulmonary arterial smooth muscle cells (PASMCs). Recent studies show that canonical transient receptor potential channel 6 (TRPC6) genes, which encode receptor-operated cation channels (ROCC) in PASMCs, play an important role in Ca2+ regulation and cell proliferation. The aim of the present study was to investigate the role of TRPC6 in monocrotaline (MCT)-induced pulmonary artery hypertension. Sprague-Dawley rats were randomly divided into normal control group and MCT group. In MCT group, pulmonary arterial hypertension was induced by a single intraperitoneal injection of MCT at a dose of 60 mg/kg. After 3 weeks, the right ventricular systolic pressure (RVSP) and the right ventricular mass index (RVMI) were measured. The lung sections were stained by HE and observed under light microscope. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) and Western blot were performed to detect the expression of TRPC6 in rat pulmonary arteries. The 1-oleoyl-2-acetyl-sn-glycerol (OAG)-induced contractile tension of pulmonary arteries were measured by vascular ring tension analysis and the intracellular Ca2+ concentration ([Ca2+](i))of PASMCs was monitored using Fluo3-AM assay. The results showed that RVSP and RVMI markedly elevated in MCT group (P<0.01) in comparison to CON group. The thickness of pulmonary vascular smooth muscles was increased and the inner diameter of pulmonary arteries was diminished in MCT group. Though there was no significant difference in the levels of mRNA and protein of TRPC6 between CON and MCT groups, the application of OAG, which can directly activate ROCC, induced greater contraction tension of pulmonary arteries (P<0.01) and more Ca2+ entries in PASMCs (P<0.05) in MCT group compared to those in control group. These results indicate that MCT induces pulmonary artery hypertension and thus remodeling of the right ventricle and pulmonary arteries in rats. The expression of mRNA and protein of TRPC6 is not potentiated by MCT, but the TRPC6/ROCC-mediated Ca2+ entry in PASMCs and vascular tone of pulmonary arteries are significantly increased with MCT treatment.

Magnon-tuning non-volatile magnetic dynamics in a CoZr/PMN-PT structure.

Magnon-tuning non-volatile magnetic dynamics is investigated in a CoZr/PMN-PT structure by measuring ferromagnetic resonance at room temperature. The electric-field control of ferromagnetic resonance shows loop-like behavior, which indicates non-volatile electric-field control of the magnetism. Further, fitting the curves of in-plane rotating angle versus ferromagnetic resonance field under different electric fields shows that the effective magnetic field changes in loop-like manner with the electric field. The resulting change in non-volatile saturation magnetization with electric field is consistent with that of a polarization electric field curve. A 1.04% change of saturation magnetization is obtained, which can be attributed to a magnon-driven magnetoelectric coupling at the CoZr/PMN-PT interface. This magnon-driven magnetoelectric coupling and its dynamic magnetic properties are significant for developing future magnetoelectric devices.

Genetic and heterosis analysis for important agronomic traits of Chinese vegetable mustard (Brassica juncea) in different environments.

Genetic effects and genotype by environment (GE) interaction effects for some important agronomic traits of Chinese vegetable mustard were analyzed by using a genetic model including additive, dominance, additive x additive effects and their interaction effects with the environment. Four variations of Chinese vegetable mustard as parental lines and their F(1s), F(2s) were evaluated in two locations. It was revealed that the agronomic traits of Chinese vegetable mustard were mainly controlled by genetic effects except plant weight (PW) and leaf weight (LW) were observed to be more affected by GE interaction effects. Among the genetic effects, additive effects took the main proportion for tiller number (TN), leaf number (LN), leaf breadth (LB) and LW; dominance effects were the main components of PW, leaf length (LL), root weight (RW) and plant height (PH); additive x additive effects were the main components of plant breadth (PB). Among the GE interaction effects, additive x environment interaction effects mainly affected LB, LW and RW, while PW, LL, PH and PB were mainly controlled by dominance x environment interaction effects. Besides, additive x additive x environment interaction was the main factor, which controlled TN and LN of Chinese vegetable mustard. For heterosis analyses, TN, LN, LB and LW of Chinese vegetable mustard showed positive H(PM) and negative H(PB). The other traits showed positive H(PM) and H(PB). Heterosis arising from GE interaction was found to varying degree for different environments. It was shown that genetic heterosis and GE interaction effects were important factors for agronomic traits in Chinese vegetable mustard.

Mitochondrial atpA gene is altered in a new orf220-type cytoplasmic male-sterile line of stem mustard (Brassica juncea).

The purpose of this research is to identify the probable mitochondrial factor associated with cytoplasmic male sterility (cms) by comparative analysis of cms and its isogenic maintainer lines in stem mustards. Dramatic variations in the morphology of floral organs were observed in cms stem mustard. Mitochondrial atpA gene was shown to be altered in cms compared with that in its maintainer line, of which mitochondrial atpA gene from its maintainer line was sequenced to encode 507 amino acids. It was indicative of high homology with mitochondrial atpA genes from other species, even as high as 94% in similarity with Oryza sativa in terms of amino acid constituents. However, only 429 amino acids were deduced in cms showing 83% similarity with atpA gene from its maintainer line. Two copies were observed in its maintainer line, but only one was found in cms. Such numerous differences of mitochondrial atpA gene between cms and its maintainer lines may not be the results of evolutionary divergence but the rearrangements of mitochondria. Expression of mitochondrial atpA gene was shown to be down-regulated in cms by using Northern blot. Consequently, mitochondrial ATP synthesis was severely decreased more than one fold in cms stem mustard indicating deficiency in mitochondrial ATP synthesis in this type of cms. Therefore, we deduced that mitochondrial atpA gene altered in cms could be associated with male-sterility in this type of cms.

Mitochondrial nad2 gene is co-transcripted with CMS-associated orfB gene in cytoplasmic male-sterile stem mustard (Brassica juncea).

The transcriptional patterns of mitochondrial respiratory related genes were investigated in cytoplasmic male-sterile and fertile maintainer lines of stem mustard, Brassica juncea. There were numerous differences in nad2 (subunit 2 of NADH dehydrogenase) between stem mustard CMS and its maintainer line. One novel open reading frame, hereafter named orfB gene, was located at the downstream of mitochondrial nad2 gene in the CMS. The novel orfB gene had high similarity with YMF19 family protein, orfB in Raphanus sativus, Helianthus annuus, Nicotiana tabacum and Beta vulgaris, orfB-CMS in Daucus carota, atp8 gene in Arabidopsis thaliana, 5' flanking of orf224 in B. napus (nap CMS) and 5' flanking of orf220 gene in CMS Brassica juncea. Three copies probed by specific fragment (amplified by primers of nad2F and nad2R from CMS) were found in the CMS line following Southern blotting digested with HindIII, but only a single copy in its maintainer line. Meanwhile, two transcripts were shown in the CMS line following Northern blotting while only one transcript was detected in the maintainer line, which were probed by specific fragment (amplified by primers of nad2F and nad2R from CMS). Meanwhile, the expression of nad2 gene was reduced in CMS bud compared to that in its maintainer line. We thus suggested that nad2 gene may be co-transcripted with CMS-associated orfB gene in the CMS. In addition, the specific fragment that was amplified by primers of nad2F and nad2R just spanned partial sequences of nad2 gene and orfB gene. Such alterations in the nad2 gene would impact the activity of NADH dehydrogenase, and subsequently signaling, inducing the expression of nuclear genes involved in male sterility in this type of cytoplasmic male sterility.

MCOLN1 Promotes Proliferation and Predicts Poor Survival of Patients with Pancreatic Ductal Adenocarcinoma.

BACKGROUND: MCOLN1 (mucolipin subfamily, member 1) was first identified as an autophagic regulator, which was essential for efficient fusion of both autophagosomes and late endosomes with lysosomes. This study is aimed at investigating the role of MCOLN1 in the development of pancreatic ductal adenocarcinoma (PDAC). METHODS: Immunohistochemistry (IHC) assay was conducted to evaluate the expression level of MCOLN1 in 82 human PDAC tumor tissues. Overall survival (OS) and recurrence-free survival (RFS) analysis was performed to assess the prognosis of patients. Colony formation and MTT assays [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide] were performed to measure the proliferation capacity of tumor cells. The expression level of related genes was measured by RT-PCR (reverse transcription polymerase chain reaction) and western blot assays. The animal model was used to examine the effects of indicated protein on tumorigenesis in vivo. RESULTS: The results of IHC showed that a high level of MCOLN1 expression was associated with the poor clinical characteristics of PDAC patients. OS and RFS were significantly worse in patients with high MCOLN1 expression. Silencing of MCOLN1 dramatically blocked the proliferation of PDAC cells. Mechanism studies confirmed that knockdown of MCOLN1 decreased the expression of Ki67 and PCNA (proliferating cell nuclear antigen), two markers of cell proliferation. In vivo, MCOILN1 depletion reduced the formation and growth of tumors in mice. CONCLUSION: The high level of MCOLN1 expression was associated with poor clinical outcomes of PDAC patients. MCOLN1 ablation could inhibit PDAC proliferation of both in vitro and in vivo, which provide a new insight and novel therapeutic target for the treatment of PDAC.

A mitochondria-targeted iridium(iii)-based photoacid generator induces dual-mode photodynamic damage within cancer cells.

A mitochondria-targeted photodynamic therapy (PDT) agent was designed and synthesized. Upon light irradiation, it can produce photoacid and its photolysis products can further sensitize 1O2 generation, causing dual-mode (oxygen-independent and oxygen-dependent) photodynamic damage in mitochondria and killing cancer cells effectively even under hypoxic conditions.

Relationship between cytoplasmic male sterility and SPL-like gene expression in stem mustard.

We studied how mitochondria-nuclear interactions may give rise to cytoplasmic male sterility (CMS) in stem mustard exhibiting abnormal microsporogenesis. In this system, expression of SPL-like, the counterpart of the Arabidopsis nuclear gene SPOROCYTELESS, is specifically lost in buds of CMS plants. When mitochondrial-specific inhibitors were applied to wild-type fertile stem mustard plants, expression of SPL-like was repressed to some extent. As a consequence, the shape and vigor of pollen grains were severely affected, whereas the fertility of pistils remained unaltered. Thereby, we suggest that a probable pathway responsible for CMS in stem mustard involves mitochondrial retrograde regulation, with SPL-like as a target nuclear gene for a mitochondrial signal.

Activation of c-Jun/JNK signaling predicts poor prognosis in nasopharyngeal carcinoma.

A significant proportion of patients with nasopharyngeal carcinoma (NPC) will develop regional relapse or distant metastasis after treatment. This present study evaluated the role of c-Jun/JNK signaling pathways in NPC and its relationship with prognosis. Our study enrolled 122 patients diagnosed with NPC and 136 chronic nasosinusitis patients. Immunohistochemistry was applied to detect positive expression of c-Jun, JNK, p-c-Jun, and p-JNK proteins. Receiver operating characteristic (ROC) curve was then adopted to assess the diagnostic value of c-Jun/JNK signaling pathways for NPC. Activated c-Jun/JNK signaling pathways were observed in NPC patients. Activation of c-Jun/JNK signaling was associated with TNM staging of NPC, as NPC patients with stage III-IV had higher positive expression rates of c-Jun, JNK, p-c-Jun, and p-JNK proteins compared to NPC patients with stage I-II. According to ROC curve results, areas under the curve of c-Jun, JNK, p-c-Jun, and p-JNK protein expression were 0.943, 0.968, 0.963, and 0.938, respectively. The 1-, 3-, and 5-year survival rates and mean survival times of dead patients were lower and shorter in patients with positive expressions of c-Jun, JNK, p-c-Jun, and p-JNK than those with negative expression (all P < 0.05). Overexpression of c-Jun/JNK is associated with development and progression of NPC, indicating that c-Jun/JNK serves as a predictive indicator for early diagnosis and prognosis of NPC.

Long intergenic noncoding RNA 01296 aggravates gastric cancer cells progress through miR-122/MMP-9.

Long non-coding RNAs (lncRNAs) play important roles on tumor development and progression in gastric cancer (GC). However, the biological function and regulatory mechanisms of LINC01296 in GC still remain unknown. The objective of this study is to investigate the clinical significance and pathological roles of LINC01296 in GC. Results showed that LINC01296 was up-regulated in GC tissue and correlated with poor prognosis. In vitro, LINC01296 knockdown was up-regulated in GC cells and LINC01296 knockdown suppressed GC cells proliferation, migration and invasion, and promoted apoptosis. In vivo xenograft assays, results showed LINC01296 knockdown significantly inhibited GC tumor growth. Bioinformatics analysis revealed that LINC01296 sponged miR-122, which was proved to target MMP-9. Western blot and RT-PCR showed that LINC01296 was positively correlated with MMP-9 expression, while miR-122 was negatively correlated to it. Overall, results indicate that LINC01296 acts as oncogenic lncRNA in GC carcinogenesis, suggesting the LINC01296/miR-122/MMP-9 regulatory pathway in GC tumorigenesis.

Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria.

The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.

Cyclometalated iridium(iii) complexes induce mitochondria-derived paraptotic cell death and inhibit tumor growth in vivo.

The development of iridium complexes as potent anticancer agents has received increasing attention in recent years. In this study, four cyclometalated Ir(iii) complexes with good photophysical properties and potent anticancer activity have been synthesized and characterized. They are taken up by human lung adenocarcinoma A549 cells very quickly and specifically target mitochondria. Mechanism studies reveal that one of them, namely IrM2, induces paraptosis accompanied by excessive mitochondria-derived cytoplasmic vacuoles. Meanwhile, IrM2 affects the ubiquitin-proteasome system (UPS) and mitogen-activated protein kinase (MAPK) signaling pathways. Furthermore, IrM2 rapidly induces a series of mitochondria-related dysfunctional events, including the loss of mitochondrial membrane potential, cellular ATP depletion, mitochondrial respiration inhibition and reactive oxygen species (ROS) elevation. The rapid loss of mitochondrial functions, elevation of ROS and impairment of the UPS induced by IrM2 lead to the collapse of mitochondria and the subsequent cytoplasmic vacuolation before the cells are ready to start the mechanisms of apoptosis and/or autophagy. Among the ROS, superoxide anion radicals play a critical role in IrM2-mediated cell death. In vivo studies reveal that IrM2 can significantly inhibit tumor growth in a mouse model. This work gives useful insights into the design and anticancer mechanisms of new metal-based anticancer agents.

[Mechanism of cytoplasmic male-sterility modulated by mitochondrial retrograde regulation in higher plants].

The type of cytoplasmic male-sterility, cytoplasmic male-sterility related mitochondrial factors, and nuclear restored gene-regulated mitochondrial factors in higher plants are reviewed in this paper. Based on gene regulation network for cytoplasmic male-sterility occurrence, we discussed and hypothesized that the interactions between nucleus and mitochondria determine cytoplasmic male-sterility occurrence modulated by mitochondrial retrograde regulation through possible mitochondrial retrograde signaling.

Genome Size Diversity in Lilium (Liliaceae) Is Correlated with Karyotype and Environmental Traits.

Genome size (GS) diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood. We performed a comprehensive study involving phylogenetically independent analysis on 71 species to explore the diversity and evolution of GS and its correlation with karyological and environmental traits within Lilium (including Nomocharis). The strong phylogenetic signal detected for GS in the genus provides evidence consistent with that the repetitive DNA may be the primary contributors to the GS diversity, while the significant positive relationships detected between GS and the haploid chromosome length (HCL) provide insights into patterns of genome evolution. The relationships between GS and karyotypes indicate that ancestral karyotypes of Lilium are likely to have exhibited small genomes, low diversity in centromeric index (CVCI) values and relatively high relative variation in chromosome length (CVCL) values. Significant relationships identified between GS and annual temperature and between GS and annual precipitation suggest that adaptation to habitat strongly influences GS diversity. We conclude that GS in Lilium is shaped by both neutral (genetic drift) and adaptive evolution. These findings will have important consequences for understanding the evolution of giant plant genomes, and exploring the role of repetitive DNA fraction and chromosome changes in a plant group with large genomes and conservation of chromosome number.