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1.
BMC Plant Biol ; 20(1): 20, 2020 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-31931714

RESUMO

BACKGROUND: Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum). RESULTS: In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K+ stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K+ uptake in a yeast mutant. CONCLUSIONS: This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K+ supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum.

2.
Plant Biotechnol J ; 2020 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-31975524

RESUMO

Kenaf is an annual crop that is widely cultivated as a source of bast (phloem) fibres, the phytoremediation of heavy metal-contaminated farmlands and textile-relevant compounds. Leaf shape played a unique role in kenaf improvement, due to the inheritance as a single locus and the association with fibre development in typical lobed-leaf varieties. Here we report a high-quality genome assembly and annotation for var. 'Fuhong 952' with 1078 Mbp genome and 66 004 protein-coding genes integrating single-molecule real-time sequencing, a high-density genetic map and high-throughput chromosome conformation capture techniques. Gene mapping assists the identification of a homeobox transcription factor LATE MERISTEM IDENTITY 1 (HcLMI1) gene controlling lobed-leaf. Virus-induced gene silencing (VIGS) of HcLMI1 in a lobed-leaf variety was critical to induce round (entire)-like leaf formation. Candidate genes involved in cell wall formation were found in quantitative trait loci (QTL) for fibre yield and quality-related traits. Comparative genomic and transcriptome analyses revealed key genes involved in bast fibre formation, among which there are twice as many cellulose synthase A (CesA) genes due to a recent whole-genome duplication after divergence from Gossypium. Population genomic analysis showed two recent population bottlenecks in kenaf, suggesting domestication and improvement process have led to an increase in fibre biogenesis and yield. This chromosome-scale genome provides an important framework and toolkit for sequence-directed genetic improvement of fibre crops.

3.
New Phytol ; 225(5): 2122-2139, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31657467

RESUMO

Group 1 Remorins (REMs) are extensively involved in virus trafficking through plasmodesmata (PD). However, their roles in Potyvirus cell-to-cell movement are not known. The plasma membrane (PM)-associated Ca2+ binding protein 1 (PCaP1) interacts with the P3N-PIPO of Turnip mosaic virus (TuMV) and is required for TuMV cell-to-cell movement, but the underlying mechanism remains elusive. The mutant plants with overexpression or knockout of REM1.2 were used to investigate its role in TuMV cell-to-cell movement. Arabidopsis thaliana complementary mutants of pcap1 were used to investigate the role of PCaP1 in TuMV cell-to-cell movement. Yeast-two-hybrid, bimolecular fluorescence complementation, co-immunoprecipitation and RT-qPCR assays were employed to investigate the underlying molecular mechanism. The results show that TuMV-P3N-PIPO recruits PCaP1 to PD and the actin filament-severing activity of PCaP1 is required for TuMV intercellular movement. REM1.2 negatively regulates the cell-to-cell movement of TuMV via competition with PCaP1 for binding actin filaments. As a counteractive response, TuMV mediates REM1.2 degradation via both 26S ubiquitin-proteasome and autophagy pathways through the interaction of VPg with REM1.2 to establish systemic infection in Arabidopsis. This work unveils the actin cytoskeleton and PM nanodomain-associated molecular events underlying the cell-to-cell movement of potyviruses.

4.
Plant Cell Physiol ; 2019 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-31830269

RESUMO

WRKY is one of the largest transcription factor families in plants, and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) with three alleles and 41 (26.6%) with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes which were accompanied by variations in intron sizes. Phylogenetic and collinearity analysis revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, 4 genes not expressed in any tissues, and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane Saccharum spontaneum.

5.
Gigascience ; 8(12)2019 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-31782791

RESUMO

BACKGROUND: Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS: Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS: This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.

6.
Nat Genet ; 51(10): 1549-1558, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31570895

RESUMO

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.


Assuntos
Ananas/genética , Produtos Agrícolas/genética , Domesticação , Genoma de Planta , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Característica Quantitativa Herdável , Ananas/crescimento & desenvolvimento , Bromelaínas/metabolismo , Produtos Agrícolas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Fenótipo , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Dinâmica Populacional , Açúcares/metabolismo
7.
BMC Genomics ; 20(1): 765, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640544

RESUMO

BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.


Assuntos
Agaricales/genética , Evolução Molecular , Genoma Mitocondrial/genética , Agaricales/classificação , Ascomicetos/classificação , Ascomicetos/genética , Basidiomycota/classificação , Basidiomycota/genética , DNA Mitocondrial/genética , Proteínas Fúngicas/genética , Ordem dos Genes , Variação Genética , Filogenia , Seleção Genética , Especificidade da Espécie
8.
Neural Regen Res ; 14(10): 1765-1771, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31169194

RESUMO

We previously demonstrated that overexpression of tropomyosin receptor kinase A (TrkA) promotes the survival and Schwann cell-like differentiation of bone marrow stromal stem cells in nerve grafts, thereby enhancing the regeneration and functional recovery of the peripheral nerve. In the present study, we investigated the molecular mechanisms underlying the neuroprotective effects of TrkA in bone marrow stromal stem cells seeded into nerve grafts. Bone marrow stromal stem cells from Sprague-Dawley rats were infected with recombinant lentivirus vector expressing rat TrkA, TrkA-shRNA or the respective control. The cells were then seeded into allogeneic rat acellular nerve allografts for bridging a 1-cm right sciatic nerve defect. Then, 8 weeks after surgery, hematoxylin and eosin staining showed that compared with the control groups, the cells and fibers in the TrkA overexpressing group were more densely and uniformly arranged, whereas they were relatively sparse and arranged in a disordered manner in the TrkA-shRNA group. Western blot assay showed that compared with the control groups, the TrkA overexpressing group had higher expression of the myelin marker, myelin basic protein and the axonal marker neurofilament 200. The TrkA overexpressing group also had higher levels of various signaling molecules, including TrkA, pTrkA (Tyr490), extracellular signal-regulated kinases 1/2 (Erk1/2), pErk1/2 (Thr202/Tyr204), and the anti-apoptotic proteins Bcl-2 and Bcl-xL. In contrast, these proteins were downregulated, while the pro-apoptotic factors Bax and Bad were upregulated, in the TrkA-shRNA group. The levels of the TrkA effectors Akt and pAkt (Ser473) were not different among the groups. These results suggest that TrkA enhances the survival and regenerative capacity of bone marrow stromal stem cells through upregulation of the Erk/Bcl-2 pathway. All procedures were approved by the Animal Ethical and Welfare Committee of Shenzhen University, China in December 2014 (approval No. AEWC-2014-001219).

9.
J Plast Reconstr Aesthet Surg ; 72(6): 902-908, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30630749

RESUMO

PURPOSE: To describe our experience using microsurgically fabricated, multilobed, chimeric, lateral arm (LA) flaps to reconstruct hand injuries with complex, multidigit, soft tissue defects and to evaluate the morbidity and esthetic and functional outcomes of the donor sites. METHODS: We performed a single center, retrospective analysis of 21 patients with hand wounds treated from October 2013 to February 2016. All patients underwent reconstruction using multilobed, chimeric, free, LA flaps. A self-reported questionnaire was used to assess donor site morbidity and satisfaction with the esthetic and overall functional result. Outcome measures were the Disabilities of the Arm, Shoulder and Hand (DASH) score, static 2-point discrimination score, and visual analogue scale. RESULTS: The study included 21 patients (20 males and 1 female), with an average age of 32.14 years (range 18-45 years), who sustained traumatic injuries in road traffic accidents (n = 2) or industrial devices (n = 19). The average DASH score was 28.25 ±â€¯2.3, the average 2-PD score was 7.20 ±â€¯1.30, and the average visual analogue scale (VAS) was 0.38 ±â€¯0.40. All 21 patients had sensory disorders at the donor site. Postoperative donor site complications comprised wound dehiscence (n = 1) and hematoma (n = 3). The patient-rated satisfaction score for the donor site was 5.40 ±â€¯0.90, and 70% of the patients would undergo the same surgery again. CONCLUSION: Microsurgical fabrication of multilobed, chimeric, LA flaps can exhibit sensory recovery and minimal pain but may cause hematoma and sensory disorders at the donor site. The flaps are a viable alternative for the reconstruction of complex, multidigit, soft tissue defects of the hands.


Assuntos
Retalhos de Tecido Biológico , Traumatismos da Mão/cirurgia , Retalho Perfurante , Procedimentos Cirúrgicos Reconstrutivos , Lesões dos Tecidos Moles/cirurgia , Adulto , Feminino , Dedos/fisiopatologia , Dedos/cirurgia , Traumatismos da Mão/fisiopatologia , Traumatismos da Mão/psicologia , Humanos , Masculino , Pessoa de Meia-Idade , Satisfação do Paciente , Complicações Pós-Operatórias/diagnóstico , Complicações Pós-Operatórias/fisiopatologia , Complicações Pós-Operatórias/psicologia , Procedimentos Cirúrgicos Reconstrutivos/efeitos adversos , Procedimentos Cirúrgicos Reconstrutivos/instrumentação , Procedimentos Cirúrgicos Reconstrutivos/métodos , Recuperação de Função Fisiológica , Lesões dos Tecidos Moles/fisiopatologia , Lesões dos Tecidos Moles/psicologia , Índices de Gravidade do Trauma
10.
BMC Genomics ; 20(1): 83, 2019 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-30678642

RESUMO

BACKGROUND: Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome. RESULTS: Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum. CONCLUSIONS: This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement.


Assuntos
Proteínas de Transporte de Cátions/genética , Evolução Molecular , Magnésio/metabolismo , Família Multigênica , Proteínas de Plantas/genética , Saccharum/genética , Proteínas de Transporte de Cátions/classificação , Proteínas de Transporte de Cátions/metabolismo , Ritmo Circadiano , Éxons , Expressão Gênica/efeitos dos fármacos , Genes de Plantas , Genômica , Íntrons , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Saccharum/efeitos dos fármacos , Saccharum/crescimento & desenvolvimento , Saccharum/metabolismo
11.
Plant Biotechnol J ; 17(1): 264-274, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-29878497

RESUMO

The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F1 individuals derived from S. officinarumLA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole-genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole-genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long-standing hypothesis and clarified the timing of speciation and whole-genome duplication events in Saccharum.


Assuntos
Poliploidia , Saccharum/genética , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Marcadores Genéticos/genética , Polimorfismo de Nucleotídeo Único/genética , Transcriptoma/genética
12.
Plant Biotechnol J ; 17(2): 488-498, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30051590

RESUMO

Sugarcane (Saccharum spp.) is a highly energy-efficient crop primarily for sugar and bio-ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high-quality genome-wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in-depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.


Assuntos
Genoma de Planta/genética , Genômica , Saccharum/genética , Adaptação Fisiológica , Alelos , Quimera , Variação Genética , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único/genética , Poliploidia , Saccharum/fisiologia
13.
Gigascience ; 8(12): 1–18, 2019.
Artigo | Sec. Est. Saúde SP, SESSP-IBPROD, Sec. Est. Saúde SP | ID: but-ib17279

RESUMO

Background: Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results: Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ~3.8–4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. Conclusions: This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.

14.
Nat Genet ; 50(12): 1754, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30425353

RESUMO

In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/ ." The errors have been corrected in the HTML and PDF versions of the article.

15.
BMC Plant Biol ; 18(1): 270, 2018 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-30404601

RESUMO

BACKGROUND: The SWEET (Sugars Will Eventually be Exported Transporters) gene family is a recently identified group of sugar transporters that play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction, nectar secretion, and reproductive tissue development. However, little information on Saccharum SWEET is available for this crop with a complex genetic background. RESULTS: In this study, 22 SWEET genes were identified from Saccharum spontaneum Bacterial Artificial Chromosome libraries sequences. Phylogenetic analyses of SWEETs from 11 representative plant species showed that gene expansions of the SWEET family were mainly caused by the recent gene duplication in dicot plants, while these gene expansions were attributed to the ancient whole genome duplication (WGD) in monocot plant species. Gene expression profiles were obtained from RNA-seq analysis. SWEET1a and SWEET2s had higher expression levels in the transitional zone and maturing zone than in the other analyzed zones. SWEET1b was mainly expressed in the leaf tissues and the mature zone of the leaf of both S. spontaneum and S. officinarum, and displayed a peak in the morning and was undetectable in both sclerenchyma and parenchyma cells from the mature stalks of S. officinarum. SsSWEET4a\4b had higher expression levels than SWEET4c and were mainly expressed in the stems of seedlings and mature plants. SWEET13s are recently duplicated genes, and the expression of SWEET13s dramatically increased from the maturing to mature zones. SWEET16b's expression was not detected in S. officinarum, but displayed a rhythmic diurnal expression pattern. CONCLUSIONS: Our study revealed the gene evolutionary history of SWEETs in Saccharum and SWEET1b was found to be a sucrose starvation-induced gene involved in the sugar transportation in the high photosynthetic zones. SWEET13c was identified as the key player in the efflux of sugar transportation in mature photosynthetic tissues. SWEET4a\4b were found to be mainly involved in sugar transportation in the stalk. SWEET1a\2a\4a\4b\13a\16b were suggested to be the genes contributing to the differences in sugar contents between S. spontaneum and S. officinarum. Our results are valuable for further functional analysis of SWEET genes and utilization of the SWEET genes for genetic improvement of Saccharum for biofuel production.


Assuntos
Saccharum/genética , Regulação da Expressão Gênica de Plantas , Genômica/métodos , Haplótipos/genética , Filogenia , Proteínas de Plantas/genética
16.
Nat Genet ; 50(11): 1565-1573, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30297971

RESUMO

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.


Assuntos
Genoma de Planta/genética , Poliploidia , Saccharum/genética , Alelos , Quimera/genética , Duplicação Cromossômica , Cromossomos de Plantas , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Seleção Genética , Sorghum/genética , Translocação Genética
17.
Front Plant Sci ; 9: 1414, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30319674

RESUMO

Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80-90% of the genome from S. officinarum and 10-20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.

18.
Hortic Res ; 5: 66, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30245835

RESUMO

Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism (CAM) photosynthesis. Here, we developed a pineapple genomics database (PGD, http://pineapple.angiosperms.org/pineapple/html/index.html) as a central online platform for storing and integrating genomic, transcriptomic, function annotation and genetic marker data for pineapple (Ananas comosus (L.) Merr.). The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics, gene expression, gene co-expression molecular marker, and gene annotation of A. comosus (L). PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively, bulk data download, a detailed user manual, and data integration information. PGD was developed with the capacity to integrate future data resources, and will be used as a long-term and open access database to facilitate the study of the biology, distribution, and the evolution of pineapple and the relative plant species. An email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.

19.
Front Plant Sci ; 9: 218, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29535742

RESUMO

Saccharum spontaneum is a major Saccharum species that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescence in situ hybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identify S. spontaneum individual chromosomes and study the relationship between S. spontaneum and other related species. We screened low-copy BACs as probes from the sequences of a high coverage of S. spontaneum BAC library based on BLAST search of the sorghum genome. In total, we isolated 49 positive BAC clones, and identified 27 BAC clones that can give specific signals on the S. spontaneum chromosomes. Of the 27 BAC probes, 18 were confirmed to be able to discriminate the eight basic chromosomes of S. spontaneum. Moreover, BAC-24, BAC-66, BAC-78, BAC-69, BAC-71, BAC-73, and BAC-77 probes were used to construct physical maps of chromosome 1 and chromosome 2 of S. spontaneum, which indicated synteny in Sb01 between S. spontaneum and sorghum. Furthermore, we found that BAC-14 and BAC-19 probes, corresponding to the sorghum chromosomes 2 and 8, respectively, localized to different arms of the same S. spontaneum chromosome, suggesting that there was an inter-chromosomal rearrangement event between S. spontaneum and sorghum. Our study provides the first set of chromosome-specific cytogenetic markers in Saccharum and is critical for future advances in cytogenetics and genome sequencing studies in Saccharum.

20.
J Knee Surg ; 31(8): 716-722, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28985644

RESUMO

Techniques using the anteromedial portal (AMP) and accessory anteromedial portal (AAMP) are commonly used in anterior cruciate ligament (ACL) reconstruction. The aim of this study was to investigate the radiological and clinical outcomes of arthroscopic single-bundle ACL reconstruction using the AMP or AAMP technique to drill the femoral tunnel. The records of 157 patients who underwent single-bundle ACL reconstruction using the AMP or AAMP technique between 2011 and 2015 were reviewed. The femoral tunnel clock-face position and femoral tunnel and tibial tunnel anterior-posterior (AP) inclination angles were assessed on axial or AP magnetic resonance images. At last follow-up, the Lachman test and pivot-shift test were used to evaluate AP and rotational stability, respectively. The Lysholm knee scoring scale and the International Knee Documentation Committee (IKDC) form were used to evaluate clinical and functional results. No statistically significant differences were found between the groups in patient age, sex, follow-up period, or affected side distribution. The mean femoral tunnel inclination angle was 31.13 ± 8.06 degrees in the AMP group and 30.17 ± 9.02 degrees in the AAMP group (p = 0.513). The tibial tunnel inclination angle in the AMP group (16.28 ± 7.89 degrees) was not different from that in the AAMP group (13.70 ± 6.08 degrees). No significant differences were observed between the two groups in the Lachman test, pivot-shift test, Lysholm knee scoring scale, or IKDC scores. The AAMP technique was not clinically superior to the AMP technique in ACL reconstruction. This is a retrospective comparative study and its level of evidence is III.


Assuntos
Lesões do Ligamento Cruzado Anterior/cirurgia , Reconstrução do Ligamento Cruzado Anterior/métodos , Artroscopia/métodos , Fêmur/cirurgia , Adulto , Lesões do Ligamento Cruzado Anterior/diagnóstico por imagem , Lesões do Ligamento Cruzado Anterior/fisiopatologia , Feminino , Humanos , Articulação do Joelho/diagnóstico por imagem , Articulação do Joelho/fisiopatologia , Articulação do Joelho/cirurgia , Escore de Lysholm para Joelho , Imagem por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Exame Físico , Amplitude de Movimento Articular , Estudos Retrospectivos , Tíbia/cirurgia , Resultado do Tratamento , Adulto Jovem
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