Variations and trade-offs in leaf and culm functional traits among 77 woody bamboo species.

BACKGROUND: Woody bamboos are the only diverse large perennial grasses in mesic-wet forests and are widely distributed in the understory and canopy. The functional trait variations and trade-offs in this taxon remain unclear due to woody bamboo syndromes (represented by lignified culm of composed internodes and nodes). Here, we examined the effects of heritable legacy and occurrence site climates on functional trait variations in leaf and culm across 77 woody bamboo species in a common garden. We explored the trade-offs among leaf functional traits, the connection between leaf nitrogen (N), phosphorus (P) concentrations and functional niche traits, and the correlation of functional traits between leaves and culms. RESULTS: The Bayesian mixed models reveal that the combined effects of heritable legacy (phylogenetic distances and other evolutionary processes) and occurrence site climates accounted for 55.10-90.89% of the total variation among species for each studied trait. The standardized major axis analysis identified trade-offs among leaf functional traits in woody bamboo consistent with the global leaf economics spectrum; however, compared to non-bamboo species, the woody bamboo exhibited lower leaf mass per area but higher N, P concentrations and assimilation, dark respiration rates. The canonical correlation analysis demonstrated a positive correlation (ρ = 0.57, P-value < 0.001) between leaf N, P concentrations and morphophysiology traits. The phylogenetic principal components and trait network analyses indicated that leaf and culm traits were clustered separately, with leaf assimilation and respiration rates associated with culm ground diameter. CONCLUSION: Our study confirms the applicability of the leaf economics spectrum and the biogeochemical niche in woody bamboo taxa, improves the understanding of woody bamboo leaf and culm functional trait variations and trade-offs, and broadens the taxonomic units considered in plant functional trait studies, which contributes to our comprehensive understanding of terrestrial forest ecosystems.

Climatic conditions affect shoot flammability by influencing flammability-related functional traits in nonfire-prone habitats.

Plant flammability is an important driver of wildfires, and flammability itself is determined by several plant functional traits. While many plant traits are influenced by climatic conditions, the interaction between climatic conditions and plant flammability has rarely been investigated. Here, we explored the relationships among climatic conditions, shoot-level flammability components, and flammability-related functional traits for 186 plant species from fire-prone and nonfire-prone habitats. For species originating from nonfire-prone habitats, those from warmer areas tended to have lower shoot moisture content and larger leaves, and had higher shoot flammability with higher ignitibility, combustibility, and sustainability. Plants in wetter areas tended to have lower shoot flammability with lower combustibility and sustainability due to higher shoot moisture contents. In fire-prone habitats, shoot flammability was not significantly related to any climatic factor. Our study suggests that for species originating in nonfire-prone habitats, climatic conditions have influenced plant flammability by shifting flammability-related functional traits, including leaf size and shoot moisture content. Climate does not predict shoot flammability in species from fire-prone habitats; here, fire regimes may have an important role in shaping plant flammability. Understanding these nuances in the determinants of plant flammability is important in an increasingly fire-prone world.

Variations and patterns of C and N stoichiometry in the first five root branch orders across 218 woody plant species.

Despite the vital role in carbon (C) sequestration and nutrient retention, variations and patterns in root C and nitrogen (N) stoichiometry of the first five root orders across woody plant species remains unclear. We compiled a dataset to explore variations and patterns of root C and N stoichiometry in the first five orders of 218 woody plant species. Across the five orders, root N concentrations were greater in deciduous, broadleaf, and arbuscular mycorrhizal species than in evergreen, coniferous species, and ectomycorrhizal association species, respectively. Contrasting trends were found for root C : N ratios. Most root branch orders showed clear latitudinal and altitudinal trends in root C and N stoichiometry. There were opposite patterns in N concentrations between latitude and altitude. Such variations were mainly driven by plant species, and climatic factors together. Our results indicate divergent C and N use strategies among plant types and convergence and divergence in the patterns of C and N stoichiometry between latitude and altitude across the first five root orders. These findings provide important data on the root economics spectrum and biogeochemical models to improve understanding and prediction of climate change effects on C and nutrient dynamics in terrestrial ecosystems.

Suitable coverage and slope guided by soil and water conservation can prevent non-point source pollution diffusion: A case study of grassland.

Non-point source pollution caused by surface runoff has been a popular hydrological and environmental safety issue and has attracted extensive attention from global scholars. To identify the optimal vegetation coverage of Festuca arundinacea grassland for controlling soil erosion and purifying surface runoff, bare land was chosen as the control in this experiment. Simulated rainfall experiments were carried out with three levels of coverage (low coverage, moderate coverage and full coverage) under four slope conditions (flat slope, gentle slope, medium slope, and steep slope) and at four rainfall intensities (moderate rainfall, heavy rainfall, rainstorm and heavy rainstorm). The comprehensive evaluation results suggested that the capacity of Festuca arundinacea grassland for reducing the surface runoff, sediment yield, suspended solids (SS), total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (COD) decreased with increasing rainfall intensity and slope but increased with increasing vegetation coverage. Structural equation model (SEM) results suggested that there were positive relationships between the vegetation coverage and purification capacity index and negative correlations between the rainfall intensity and slope and the purification capacity index. The response surface analysis results suggested that the optimal vegetation coverage should be higher than 84% and that the slope should be smaller than 10° for controlling soil erosion and avoiding pollution via diffusion with surface runoff in Festuca arundinacea grassland. This study proposes recommendations for the vegetation configuration pattern in the development and management of runoff purification systems.

Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarpa.

BACKGROUND: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. RESULTS: A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. CONCLUSIONS: Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.

Genome-Wide Investigation of the NF-X1 Gene Family in Populus trichocarpa Expression Profiles during Development and Stress.

Poplar are planted extensively in reforestation and afforestation. However, their successful establishment largely depends on the environmental conditions of the newly established plantation and their resistance to abiotic as well as biotic stresses. NF-X1, a widespread transcription factor in plants, plays an irreplaceable role in plant growth, development, and stress tolerance. Although the whole genome sequence of Populus trichocarpa has been published for a long time, little is known about the NF-X1 genes in poplar, especially those related to drought stress, mechanical damage, insect feeding, and hormone response at the whole genome level. In this study, whole genome analysis of the poplar NF-X1 family was performed, and 4 PtrNF-X1 genes were identified. Then, bioinformatics analysis and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, and expression patterns of PtrNF-X1genes. Sequence analysis revealed that one-quarter of the PtrNF-X1 genes did not contain introns. Phylogenetic analysis revealed that all NF-X1 genes were split into three subfamilies. The number of two pairs of segmented replication genes were detected in poplars. Cis-acting element analysis identified a large number of elements of growth and development and stress-related elements on the promoters of different NF-X1 members. In addition, some PtrNF-X1 could be significantly induced by polyethylene glycol (PEG) and abscisic acid (ABA), thus revealing their potential role in regulating stress response. Comprehensive analysis is helpful in selecting candidate NF-X1 genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.

Shoot-level flammability across the Dracophyllum (Ericaceae) phylogeny: evidence for flammability being an emergent property in a land with little fire.

Plant flammability varies across species, but the evolutionary basis for this variation is not well understood. Phylogenetic analysis of interspecific variation in flammability can provide insights into the evolution of plant flammability. We measured four components of flammability (ignitability, sustainability, combustibility and consumability) to assess the shoot-level flammability of 21 species of Dracophyllum (Ericaceae). Using a macroevolutionary approach, we explored phylogenetic patterns of variation in shoot-level flammability. Shoot-level flammability varied widely in Dracophyllum. Species in the subgenus Oreothamnus had higher flammability and smaller leaves than those in the subgenus Dracophyllum. Shoot flammability (ignitability, combustibility and consumability) and leaf length showed phylogenetic conservatism across genus Dracophyllum, but exhibited lability among some closely related species, such as D. menziesii and D. fiordense. Shoot flammability of Dracophyllum species was negatively correlated with leaf length and shoot moisture content, but had no relationship with the geographic distribution of Dracophyllum species. Shoot-level flammability varied widely in the genus Dracophyllum, but showed phylogenetic conservatism. The higher flammability of the subgenus Oreothamnus may be an incidental or emergent property as a result of the evolution of flammability-related traits, such as smaller leaves, which were selected for other functions and incidentally changed flammability.

Green firebreaks as a management tool for wildfires: Lessons from China.

Wildfire is a widespread natural hazard that is expected to increase in areal extent, severity and frequency with ongoing changes in climate and land-use. One tool that has been used in an effort to reduce the damage caused by wildfires is green firebreaks: strips of low-flammability vegetation grown at strategic locations in the landscape. Green firebreaks are increasingly being recommended for wildfire management and have been implemented in many countries. The approach is particularly widely used in China, where more than 364,000 km of green firebreaks have been planted and a further 167,000 km are planned for construction before 2025. China is not only a world leader in the implementation of green firebreaks but has also led the way in testing the effectiveness of green firebreaks and in providing guidelines for green firebreak construction. However, most of this research has been reported in the non-English literature, and so is inaccessible to many readers. Here we review the extensive research on the construction and effectiveness of green firebreaks in China and examine how the lessons learned from this research could contribute to the effective implementation of green firebreaks globally. Chinese studies suggest that the ideal species for green firebreaks should meet trait requirements from three perspectives: ecological, silvicultural and economic. Green firebreaks with a multi-layered structure and a closed canopy have the potential to be an effective, long-term, biodiversity-friendly and low-cost tool for fire suppression, although they complement rather than replace other more traditional fire suppression approaches.

Discovery and annotation of a novel transposable element family in Gossypium.

BACKGROUND: Fluorescence in situ hybridization (FISH) is an efficient cytogenetic technology to study chromosome structure. Transposable element (TE) is an important component in eukaryotic genomes and can provide insights in the structure and evolution of eukaryotic genomes. RESULTS: A FISH probe derived from bacterial artificial chromosome (BAC) clone 299N22 generated striking signals on all 26 chromosomes of the cotton diploid A genome (AA, 2x=26) but very few on the diploid D genome (DD, 2x=26). All 26 chromosomes of the A sub genome (At) of tetraploid cotton (AADD, 2n=4x=52) also gave positive signals with this FISH probe, whereas very few signals were observed on the D sub genome (Dt). Sequencing and annotation of BAC clone 299N22, revealed a novel Ty3/gypsy transposon family, which was named as 'CICR'. This family is a significant contributor to size expansion in the A (sub) genome but not in the D (sub) genome. Further FISH analysis with the LTR of CICR as a probe revealed that CICR is lineage-specific, since massive repeats were found in A and B genomic groups, but not in C-G genomic groups within the Gossypium genus. Molecular evolutionary analysis of CICR suggested that tetraploid cottons evolved after silence of the transposon family 1-1.5 million years ago (Mya). Furthermore, A genomes are more homologous with B genomes, and the C, E, F, and G genomes likely diverged from a common ancestor prior to 3.5-4 Mya, the time when CICR appeared. The genomic variation caused by the insertion of CICR in the A (sub) genome may have played an important role in the speciation of organisms with A genomes. CONCLUSIONS: The CICR family is highly repetitive in A and B genomes of Gossypium, but not amplified in the C-G genomes. The differential amount of CICR family in At and Dt will aid in partitioning sub genome sequences for chromosome assemblies during tetraploid genome sequencing and will act as a method for assessing the accuracy of tetraploid genomes by looking at the proportion of CICR elements in resulting pseudochromosome sequences. The timeline of the expansion of CICR family provides a new reference for cotton evolutionary analysis, while the impact on gene function caused by the insertion of CICR elements will be a target for further analysis of investigating phenotypic differences between A genome and D genome species.

Habitat differentiation and environmental adaptability contribute to leaf size variations globally in C3 and C4 grasses.

The grass family (Poaceae) dominates ~43 % of Earth's land area and contributes 33 % of terrestrial primary productivity that is critical to naturally regulating atmosphere CO2 concentration and global climate change. Currently grasses comprise ~11,780 species and ~50 % of them (~6000 species) utilize C4 photosynthetic pathway. Generally, grass species have smaller leaves under colder and drier environments, but it is unclear whether the primary drivers of leaf size differ between C3 and C4 grasses on a global scale. Here, we analyzed 34 environmental variables, such as latitude, elevation, mean annual temperature, mean annual precipitation, and solar radiation etc., through a comparatively comprehensive database of ~3.0 million occurrence records from 1380 C3 and 978 C4 grass species (2358 species in total). Results from this study confirm that C4 grasses have occupied habitats with lower latitudes and elevations, characterized by warmer, sunnier, drier and less fertile environmental conditions. Grass leaf size correlates positively with mean annual temperature and precipitation as expected. Our results also demonstrate that the mean temperature of the wettest quarter of the year is the primary control for C3 leaf size, whereas C4 leaf size is negatively correlated with the difference between summer and winter temperatures. For C4 grasses, phylogeny exerts a significant effect on leaf size but is less important than environmental factors. Our findings highlight the importance of evolutionarily contrasting variations in leaf size between C3 and C4 grasses for shaping their geographical distribution and habitat suitability at the global scale.

Rapid Evaluation of Material Surface Modification by a Dielectric Barrier Discharge Based on Fluorescence Coloring and Image Processing Technologies.

In recent years, improving the surface properties of large-scale insulation by plasma modification has attracted extensive attention with the development of power systems and high-tech industries. However, routine evaluations of the modification effect and uniformity require complicated tests after the plasma is powered off, which waste a lot of time and cannot regulate the modification effect online. In this study, a novel fluorescence-assisted dielectric barrier discharge (DBD) for fabricating a functional film is developed, and a rapid evaluation method of the modification effect and uniformity is proposed based on fluorescence coloring and image processing technologies. The results show that the addition of an organic fluorescent agent in the DBD with hexamethyldisiloxane (HMDSO) has no negative effect on the plasma discharge and modification effect, and the fluorescence-assisted DBD successfully fabricates the functional films with typical chromogenic groups (N-H and S═O) that exhibit typical fluorescence under an UV lamp. According to image processing and parameter extraction, the plasma-assisted fluorescent film is converted into a two-dimensional (2D) color map with nine color levels, and three characteristic parameters are proposed to evaluate the modification effect rapidly and directly. It shows that the warmer the color of the treated sample, the better the hydrophobicity and electrical insulating properties, where the red region represents the optimally modified surface, while the blue region represents the worst one. The area, shape, and integrity of the plasma modification are clarified quantificationally, which provides the possibility of further online evaluation of the modification effect and uniformity by the plasma treatment.

Drought stress drives sex-specific differences in plant resistance against herbivores between male and female poplars through changes in transcriptional and metabolic profiles.

Drought stress poses adverse influence on plant growth and further alters plant-herbivore interactions. Such effect is enhanced as drought occurrence is reported to increase due to global warming. Although dioecious plant species have shown sex-specific response to drought stress through the changes in growth performance and stress tolerance, whether such changes will drive sex-specific differences in defense against herbivores between male and female plant conspecifics is barely studied. In the current study, female and male poplar full-siblings were submitted to moderate (75 % field water capacity) and severe drought (50 % field water capacity) stresses, followed by herbivore growth and feeding bioassays to test the effect of plant gender on herbivore growth and feeding performance of two specialist and two generalist leaf herbivores. The results showed that although the growth of both plant sexes was inhibited by the two drought levels, male plants performed better than female conspecifics. In the paired-choice bioassays, the specialist herbivores preferred female plants while the generalist herbivores fed more on the male plants without drought stress. Both the moderate and severe drought stresses reversed such preferences. In the triple-choice bioassays, the specialist herbivores preferred female control plants while the generalist herbivores fed more on female plants under severe drought. In addition, the specialist herbivores fed on female plants from severe drought stress grew the worst while the generalist herbivores gained the highest fresh weight. The transcriptomic and metabolomic profiling revealed that female plant leaves contained higher levels of flavonoids than males under control condition while severe drought stress remarkably reduced the levels of defensive metabolites such as flavonoids, isoflavonoids, neoflavonoids and alkaloids in female but not in male plant leaves.

External application of nitrogen alleviates toxicity of cadmium on poplars via starch and sucrose metabolism.

Phytoremediation technology can help achieve moderate cost and considerable effect with respect to the remediation of heavy metal (HM) pollution in soil and water. Many previous studies have suggested the role of nitrogen (N) in the alleviation of effects of HM on plants. Herein, we sought to determine the molecular mechanisms by which additional N supplementation mitigates cadmium (Cd) toxicity in poplars using a combination of physiological, transcriptomic and phosphoproteomic analyses. The application of N can alleviate the toxicity of Cd to Populus by reducing chlorophyll degradation, maintaining the stability of ions inside and outside the cell membrane and increasing the soluble sugar content. Plant samples from the control, Cd stress and Cd_N treatments were used for an integrated analysis of the transcriptome, as well as for phosphoproteomics analysis. Moreover, 1314 differentially expressed genes and 119 differentially expressed kinase genes were discovered. Application of additional N under Cd stress promoted the phosphorylation process. Furthermore, 51 significantly enriched phosphorylated protein sites and 23 differentially expressed kinases were identified using phosphoproteomic and proteomic analyses. Importantly, transcriptomic and phosphoproteomic analyses jointly determined that the application of N could activate corresponding gene expression [UDP-glucose-dehydrogenase (UGD), GAUT, PME, pectin lyase, UDP-glucose-pyrophosphorylase 2 (UGP2), sucrose phosphate synthase (SPS), SUS and SPP2] and protein phosphorylation (UGP2 and SPS) in the sugar and starch synthesis pathways, which promoted the synthesis of sucrose and soluble sugar and subsequently alleviated the damage caused by Cd.

MiR-30c-5p/ROCK2 axis regulates cell proliferation, apoptosis and EMT via the PI3K/AKT signaling pathway in HG-induced HK-2 cells.

Diabetic nephropathy (DN) is one of the most common complications of diabetes mellitus. Increasing evidence suggests that microRNA-30c-5p (miR-30c-5p) participates in the pathogenesis of DN, but the mechanism has not been clearly understood. Therefore, this study aimed to investigate the biological role of miR-30c-5p in human DN progression in vitro. Compared with the controls, DN tissues and high glucose-induced HK-2 cells had significantly reduced miR-30c-5p levels, while ROCK2 expression was prominently elevated. Additionally, the miR-30c-5p mimic distinctly facilitated cell proliferation and blocked cell apoptosis and epithelial-mesenchymal transition (EMT). However, ROCK2 was a target gene of miR-30c-5p, and the effects of miR-30c-5p mimic on cell proliferation, apoptosis and EMT were reversed by ROCK2 upregulation in vitro. Furthermore, the pathogenesis of DN was regulated by the miR-30c-5p/ROCK2 axis via the PI3K/AKT pathway. MiR-30c-5p regulating cell proliferation, apoptosis and EMT through targeting ROCK2 via the PI3K/AKT pathway provides the novel potential target for clinical treatment of DN.

Identification of a genome-specific repetitive element in the Gossypium D genome.

The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.

Shoot flammability of vascular plants is phylogenetically conserved and related to habitat fire-proneness and growth form.

Terrestrial plants and fire have interacted for at least 420 million years1. Whether recurrent fire drives plants to evolve higher flammability and what the evolutionary pattern of plant flammability is remain unclear2-7. Here, we show that phylogeny, the susceptibility of a habitat to have recurrent fires (that is, fire-proneness) and growth form are important predictors of the shoot flammability of 194 indigenous and introduced vascular plant species (Tracheophyta) from New Zealand. The phylogenetic signal of the flammability components and the variation in flammability among phylogenetic groups (families and higher taxonomic level clades) demonstrate that shoot flammability is phylogenetically conserved. Some closely related species, such as in Dracophyllum (Ericaceae), vary in flammability, indicating that flammability exhibits evolutionary flexibility. Species in fire-prone ecosystems tend to be more flammable than species from non-fire-prone ecosystems, suggesting that fire may have an important role in the evolution of plant flammability. Growth form also influenced flammability-forbs were less flammable than grasses, trees and shrubs; by contrast, grasses had higher biomass consumption by fire than other groups. The results show that shoot flammability of plants is largely correlated with phylogenetic relatedness, and high flammability may result in parallel evolution driven by environmental factors, such as fire regime.

A Gossypium BAC clone contains key repeat components distinguishing sub-genome of allotetraploidy cottons.

BACKGROUND: Dissecting genome organization is indispensable for further functional and applied studies. As genome sequences data shown, cotton genomes contain more than 60 % repetitive sequences, so study on repetitive sequences composition, structure, and distribution is the key step to dissect cotton genome. RESULTS: In this study, a bacterial artificial chromosome (BAC) clone enriched in repetitive sequences, was discovered initiatively by fluorescence in situ hybridization (FISH). FISHing with allotetraploidy cotton as target DNA, dispersed signals on most regions of all A sub-genome chromosomes, and only middle regions of all D sub-genome chromosomes were detected. Further FISHing with other cotton species bearing A or D genome as target DNA, specific signals were viewed. After BAC sequencing and bioinformational analysis, 129 repeat elements, size about 57,172 bp were found, accounting for more than 62 % of the BAC sequence (91,238 bp). Among them, a type of long terminal repeat-retrotransposon (LTR-RT), LTR/Gypsy was the key element causing the specific FISH results. Using the fragments of BAC matching with the identified Gypsy-like LTR as probes, the BAC-57I23-like FISH signals were reappeared. Running BLASTN, the fragments had good match with all chromosomes of G. arboreum (A2) genome and A sub-genome of G. hirsutum (AD1), and had relatively inferior match with all chromosomes of D sub-genome of AD1, but had little match with the chromosomes of G. raimondii (D5) genome, which was consistent with the FISH results. CONCLUSION: A repeats-enriched cytogenetic marker to identify A and D sub-genomes of Gossypium was discovered by FISH. Combined sequences analysis with FISH verification, the assembly quality of repetitive sequences in the allotetraploidy cotton draft genome was assessed, and better chromosome belonging was verified. We also found the genomic distribution of the identified Gypsy-LTR-RT was similar to the distribution of heterochromatin. The expansion of this type of Gypsy-LTR-RT in heterochromatic regions may be one of the major reasons for the size gap between A and D genome. The findings showed here will help to understand the composition, structure, and evolution of cotton genome, and contribute to the further perfection of the draft genomes of cotton.

Screening and chromosome localization of two cotton BAC clones.

Two bacterial artificial chromosome (BAC) clones (350B21 and 299N22) of Pima 90-53 cotton [Gossypium barbadense Linnaeus, 1753 (2n=4x=52)] were screened from a BAC library using SSR markers. Strong hybridization signals were detected at terminal regions of all A genome (sub-genome) chromosomes, but were almost absent in D genome (sub-genome) chromosomes with BAC clone 350B21 as the probe. The results indicate that specific sequences, which only exist at the terminal parts of A genome (sub-genome) chromosomes with a huge repeat number, may be contained in BAC clone 350B21. When utilizing FISH with the BAC clone 299N22 as probe, a pair of obvious signals was detected on chromosome 13 of D genome (sub-genome), while strong dispersed signals were detected on all A genome (sub-genome) chromosomes. The results showed that peculiar repetitive sequence, which was distributed throughout all A genome (sub-genome) chromosomes, may exist in BAC clone 299N22. The absence of the repetitive sequences, which exist in the two BAC clones, in D genome may account for the genome-size variation between A and D genomes. In addition, the microcolinearity analysis of the clone 299N22 and its homologous region on Gossypium raimondii Ulbrich, 1932 chromosome 13 (D513) indicated that the clone 299N22 might come from A sub-genome of sea island cotton (Gossypium barbadense), and a huge number of small deletions, illegitimate recombination, translocation and rearrangements may have occurred during the genus evolution. The two BAC clones studied here can be used as cytological markers but will be also be helpful to research in cotton genome evolution and comparative genomics.

Construction of cytogenetic map of Gossypium herbaceum chromosome 1 and its integration with genetic maps.

BACKGROUND: Cytogenetic map can provide not only information of the genome structure, but also can build a solid foundation for genetic research. With the developments of molecular and cytogenetic studies in cotton (Gossypium), the construction of cytogenetic map is becoming more and more imperative. RESULTS: A cytogenetic map of chromosome 1 (A101) of Gossypium herbaceum (A1) which includes 10 bacterial artificial chromosome (BAC) clones was constructed by using fluorescent in situ hybridization (FISH). Meanwhile, comparison and analysis were made for the cytogenetic map of chromosome 1 (A101) of G. herbaceum with four genetic linkage maps of chromosome 1 (Ah01) of G. hirsutum ((AD)1) and one genetic linkage map of chromosome 1 of (A101) G. arboreum (A2). The 10 BAC clones were also used to be localized on G. raimondii (D5) chromosome 1 (D501), and 2 of them showed clear unique hybridized signals. Furthermore, these 2 BAC clones were also shown localized on chromosome 1 of both A sub-genome and D sub-genome of G. hirsutum. CONCLUSION: The comparison of the cytogenetic map with genetic linkage maps showed that most of the identified marker-tagged BAC clones appearing same orders in different maps except three markers showing different positions, which might indicate chromosomal segmental rearrangements. The positions of the 2 BAC clones which were localized on Ah01 and Dh01 chromosomes were almost the same as that on A101 and D501 chromosomes. The corresponding anchored SSR markers of these 2 BAC clones were firstly found to be localized on chromosome D501 (Dh01) as they were not seen mapped like this in any genetic map reported.