Shu S

References (19)

Title : Physiological mechanism of strigolactone enhancing tolerance to low light stress in cucumber seedlings - Zhou_2022_BMC.Plant.Biol_22_30
Author(s) : Zhou X , Tan Z , Zhou Y , Guo S , Sang T , Wang Y , Shu S
Ref : BMC Plant Biol , 22 :30 , 2022
Abstract : Strigolactone is a newly discovered type of plant hormone that has multiple roles in modulating plant responses to abiotic stress. Herein, we aimed to investigate the effects of exogenous GR24 (a synthetic analogue of strigolactone) on plant growth, photosynthetic characteristics, carbohydrate levels, endogenous strigolactone content and antioxidant metabolism in cucumber seedlings under low light stress. The results showed that the application of 10 microM GR24 can increase the photosynthetic efficiency and plant biomass of low light-stressed cucumber seedlings. GR24 increased the accumulation of carbohydrates and the synthesis of sucrose-related enzyme activities, enhanced antioxidant enzyme activities and antioxidant substance contents, and reduced the levels of H(2)O(2) and MDA in cucumber seedlings under low light stress. These results indicate that exogenous GR24 might alleviate low light stress-induced growth inhibition by regulating the assimilation of carbon and antioxidants and endogenous strigolactone contents, thereby enhancing the tolerance of cucumber seedlings to low light stress.
ESTHER : Zhou_2022_BMC.Plant.Biol_22_30
PubMedSearch : Zhou_2022_BMC.Plant.Biol_22_30
PubMedID: 35027005

Title : Endophytic Fungal Community of Huperzia serrata: Diversity and Relevance to the Production of Huperzine A by the Plant Host - Cui_2021_Molecules_26_
Author(s) : Cui L , Noushahi HA , Zhang Y , Liu J , Cosoveanu A , Liu Y , Yan L , Zhang J , Shu S
Ref : Molecules , 26 : , 2021
Abstract : As the population ages globally, there seem to be more people with Alzheimer's disease. Unfortunately, there is currently no specific treatment for the disease. At present, Huperzine A (HupA) is one of the best drugs used for the treatment of Alzheimer's disease and has been used in clinical trials for several years in China. HupA was first separated from Huperzia serrata, a traditional medicinal herb that is used to cure fever, contusions, strains, hematuria, schizophrenia, and snakebite for several hundreds of years in China, and has been confirmed to have acetylcholinesterase inhibitory activity. With the very slow growth of H. serrata, resources are becoming too scarce to meet the need for clinical treatment. Some endophytic fungal strains that produce HupA were isolated from H. serrate in previous studies. In this article, the diversity of the endophytic fungal community within H. serrata was observed and the relevance to the production of HupA by the host plant was further analyzed. A total of 1167 strains were obtained from the leaves of H. serrata followed by the stems (1045) and roots (824). The richness as well as diversity of endophytic fungi within the leaf and stem were higher than in the root. The endophytic fungal community was similar within stems as well as in leaves at all taxonomic levels. The 11 genera (Derxomyces, Lophiostoma, Cyphellophora, Devriesia, Serendipita, Kurtzmanomyces, Mycosphaerella, Conoideocrella, Brevicellicium, Piskurozyma, and Trichomerium) were positively correlated with HupA content. The correlation index of Derxomyces with HupA contents displayed the highest value (CI = 0.92), whereas Trichomerium showed the lowest value (CI = 0.02). Through electrospray ionization mass spectrometry (ESI-MS), it was confirmed that the HS7-1 strain could produce HupA and the total alkaloid concentration was 3.7 ug/g. This study will enable us to screen and isolate the strain that can produce HupA and to figure out the correlation between endophytic fungal diversity with HupA content in different plant organs. This can provide new insights into the screening of strains that can produce HupA more effectively.
ESTHER : Cui_2021_Molecules_26_
PubMedSearch : Cui_2021_Molecules_26_
PubMedID: 33567664

Title : Nutritional Status and Body Composition in Wilson Disease: A Cross-Sectional Study From China - Geng_2021_Front.Nutr_8_790520
Author(s) : Geng H , Wang S , Jin Y , Cheng N , Song B , Shu S , Li B , Han Y , Gao L , Ding Z , Xu Y , Wang X , Ma Z , Sun Y
Ref : Front Nutr , 8 :790520 , 2021
Abstract : Background: Abnormal nutritional status is frequently seen in patients with chronic diseases. To date, no study has investigated the detailed characteristics of abnormal nutritional status among Wilson's disease (WD) patients in the Chinese cohort. This study aimed to describe the nutritional status of WD patients, with a particular focus on the differences between patients with different phenotypes. Methods: The study subjects comprised 119 healthy controls, 129 inpatients (hepatic subtype, n = 34; neurological subtype, n = 95) who were being treated at the affiliated hospital of the Institute of Neurology, Anhui University of Chinese Medicine. All of the subjects were assessed for body composition by using bioelectrical impedance analysis. All WD patients received anthropometry, nutritional risk screening 2002 (NRS2002), and laboratory test (hemocyte and serum biomarkers) additionally. Results: Compared with healthy controls, the fat mass and rate of total body and trunk were significantly higher in WD patients (P < 0.001), the muscle and skeletal muscle mass of total body and trunk were significantly lower in WD patients (P < 0.001). Compared with hepatic subtype patients, the fat mass and rate of total body, trunk, and limbs were significantly lower in neurological subtype patients (P<0.01); while there were no significant differences in muscle and skeletal muscle between these two subtypes. The overall prevalence of abnormal nutritional status in WD patients was 43.41% (56/129). The prevalence of high-nutritional risk and overweight in WD patients was 17.83% (23 of 129) and 25.58% (33 of 129), respectively. Compare with patients with high nutritional risk, macro platelet ratio, alkaline phosphatase, the basal metabolic rate (p < 0.05), creatinine, trunk fat rate (p < 0.01) and appendicular skeletal muscle mass (p < 0.001) were significantly higher in patients without nutritional risk (p < 0.001). Patients with a high nutritional risk tend to have a lower cholinesterase concentration (x (2) = 4.227, p < 0.05). Conclusion: Both patients with H-subtype and N-subtype are prone to have an abnormal nutritional status. Longitudinal studies are required to investigate if nutritional status and body composition could reflect prognosis in WD patients, and which of these body composition indexes contribute to malnutrition and worse prognosis.
ESTHER : Geng_2021_Front.Nutr_8_790520
PubMedSearch : Geng_2021_Front.Nutr_8_790520
PubMedID: 35036410

Title : Design, synthesis and biological evaluation of novel chalcone-like compounds as potent and reversible pancreatic lipase inhibitors - Huo_2020_Bioorg.Med.Chem__115853
Author(s) : Huo PC , Hu Q , Shu S , Zhou QH , He RJ , Hou J , Guan XQ , Tu DZ , Hou XD , Liu P , Zhang N , Liu ZG , Ge GB
Ref : Bioorganic & Medicinal Chemistry , :115853 , 2020
Abstract : Pancreatic lipase (PL), a crucial enzyme responsible for hydrolysis of dietary lipids, has been validated as a key therapeutic target to prevent and treat obesity-associated metabolic disorders. Herein, we report the design, synthesis and biological evaluation of a series of chalcone-like compounds as potent and reversible PL inhibitors. Following two rounds of structural modifications at both A and B rings of a chalcone-like skeleton, structure-PL inhibition relationships of the chalcone-like compounds were studied, while the key substituents that would be beneficial for PL inhibition were revealed. Among all tested chalcone-like compounds, compound B13 (a novel chalcone-like compound bearing two long carbon chains) displayed the most potent PL inhibition activity, with an IC(50) value of 0.33 M. Inhibition kinetic analyses demonstrated that B13 could potently inhibit PL-mediated 4-MUO hydrolysis in a mixed inhibition manner, with the K(i) value of 0.12 M. Molecular docking simulations suggested that B13 could tightly bind on PL at both the catalytic site and a non-catalytic site that was located on the surface of PL, which was consistent with the mixed inhibition mode of this agent. In addition, B13 displayed excellent stability in artificial gastrointestinal fluids and good metabolic stability in human liver preparations. Collectively, our findings suggested that chalcone-like compounds were good choices for design and development of orally administrated PL inhibitors, while B13 could be served as a promising lead compound to develop novel anti-obesity agents via targeting on PL.
ESTHER : Huo_2020_Bioorg.Med.Chem__115853
PubMedSearch : Huo_2020_Bioorg.Med.Chem__115853
PubMedID: 33214035

Title : The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization - McCormick_2018_Plant.J_93_338
Author(s) : McCormick RF , Truong SK , Sreedasyam A , Jenkins J , Shu S , Sims D , Kennedy M , Amirebrahimi M , Weers BD , McKinley B , Mattison A , Morishige DT , Grimwood J , Schmutz J , Mullet JE
Ref : Plant J , 93 :338 , 2018
Abstract : Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
ESTHER : McCormick_2018_Plant.J_93_338
PubMedSearch : McCormick_2018_Plant.J_93_338
PubMedID: 29161754
Gene_locus related to this paper: sorbi-a0a194ysf6 , sorbi-a0a1b6pnr2 , sorbi-a0a1b6qcb9 , sorbi-c5xx30 , sorbi-a0a1b6psg4 , sorbi-a0a1z5rj80 , sorbi-a0a1b6qfm2 , sorbi-a0a1b6qmu5 , sorbi-c6jru0

Title : The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution - Lang_2018_Plant.J_93_515
Author(s) : Lang D , Ullrich KK , Murat F , Fuchs J , Jenkins J , Haas FB , Piednoel M , Gundlach H , Van Bel M , Meyberg R , Vives C , Morata J , Symeonidi A , Hiss M , Muchero W , Kamisugi Y , Saleh O , Blanc G , Decker EL , van Gessel N , Grimwood J , Hayes RD , Graham SW , Gunter LE , McDaniel SF , Hoernstein SNW , Larsson A , Li FW , Perroud PF , Phillips J , Ranjan P , Rokshar DS , Rothfels CJ , Schneider L , Shu S , Stevenson DW , Thummler F , Tillich M , Villarreal Aguilar JC , Widiez T , Wong GK , Wymore A , Zhang Y , Zimmer AD , Quatrano RS , Mayer KFX , Goodstein D , Casacuberta JM , Vandepoele K , Reski R , Cuming AC , Tuskan GA , Maumus F , Salse J , Schmutz J , Rensing SA
Ref : Plant J , 93 :515 , 2018
Abstract : The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
ESTHER : Lang_2018_Plant.J_93_515
PubMedSearch : Lang_2018_Plant.J_93_515
PubMedID: 29237241
Gene_locus related to this paper: phypa-a9tc36 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : Genome evolution in the allotetraploid frog Xenopus laevis - Session_2016_Nature_538_336
Author(s) : Session AM , Uno Y , Kwon T , Chapman JA , Toyoda A , Takahashi S , Fukui A , Hikosaka A , Suzuki A , Kondo M , van Heeringen SJ , Quigley I , Heinz S , Ogino H , Ochi H , Hellsten U , Lyons JB , Simakov O , Putnam N , Stites J , Kuroki Y , Tanaka T , Michiue T , Watanabe M , Bogdanovic O , Lister R , Georgiou G , Paranjpe SS , van Kruijsbergen I , Shu S , Carlson J , Kinoshita T , Ohta Y , Mawaribuchi S , Jenkins J , Grimwood J , Schmutz J , Mitros T , Mozaffari SV , Suzuki Y , Haramoto Y , Yamamoto TS , Takagi C , Heald R , Miller K , Haudenschild C , Kitzman J , Nakayama T , Izutsu Y , Robert J , Fortriede J , Burns K , Lotay V , Karimi K , Yasuoka Y , Dichmann DS , Flajnik MF , Houston DW , Shendure J , DuPasquier L , Vize PD , Zorn AM , Ito M , Marcotte EM , Wallingford JB , Ito Y , Asashima M , Ueno N , Matsuda Y , Veenstra GJ , Fujiyama A , Harland RM , Taira M , Rokhsar DS
Ref : Nature , 538 :336 , 2016
Abstract : To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
ESTHER : Session_2016_Nature_538_336
PubMedSearch : Session_2016_Nature_538_336
PubMedID: 27762356
Gene_locus related to this paper: xenla-a0a1l8f4t7 , xenla-a0a1l8fbc6 , xenla-a0a1l8fct2 , xenla-q2tap9 , xenla-q4klb6 , xenla-q5xh09 , xenla-q6ax59 , xenla-q6dcw6 , xenla-q6irp4 , xenla-q6pad5 , xenla-q7sz70 , xenla-Q7ZXQ6 , xenla-q66kx1 , xenla-q640y7 , xenla-q642r3 , xenla-Q860X9 , xenla-BCHE2 , xenla-a0a1l8g7v4 , xenla-a0a1l8g1u7 , xenla-a0a1l8fmc5 , xenla-a0a1l8g467 , xenla-a0a1l8g4e4 , xenla-a0a1l8ga66 , xenla-a0a1l8gaw4 , xenla-a0a1l8gt68 , xenla-a0a1l8h0b2 , xenla-a0a1l8fdr1 , xenla-a0a1l8fdt7 , xenla-a0a1l8fi72 , xenla-a0a1l8fi73 , xenla-a0a1l8fi77 , xenla-a0a1l8fi96 , xenla-a0a1l8hc38 , xenla-a0a1l8hn27 , xenla-a0a1l8hry6 , xenla-a0a1l8hw96 , xenla-a0a1l8i2x6 , xenla-a0a1l8hei7 , xenla-a0a1l8gnd1 , xenla-a0a1l8i2g3 , xenla-a0a1l8hdn0 , xenla-a0a1l8h622

Title : Critical thresholds of liver function parameters for ketosis prediction in dairy cows using receiver operating characteristic (ROC) analysis - Sun_2015_Vet.Q_35_159
Author(s) : Sun Y , Wang B , Shu S , Zhang H , Xu C , Wu L , Xia C
Ref : Vet Q , 35 :159 , 2015
Abstract : BACKGROUND: Fatty liver syndrome and ketosis are important metabolic disorders in high-producing cows during early lactation with fatty liver usually preceding ketosis. To date, parameters for early prediction of the risk of ketosis have not been investigated in China. OBJECTIVE: To determine the predictive value of some parameters on the risk of ketosis in China. ANIMALS AND
METHODS: In a descriptive study, 48 control and 32 ketotic Holstein Friesian cows were randomly selected from one farm with a serum beta-hydroxybutyrate (BHBA) concentration of 1.20 mmol/L as cutoff point. The risk prediction thresholds for ketosis were determined by receiver operating characteristic (ROC) analysis.
RESULTS: In line with a high BHBA concentration, blood glucose concentration was significantly lower in ketotic cows compared to control animals (2.77 +/- 0.24 versus 3.34 +/- 0.03 mmol/L; P = 0.02). Thresholds were more than 0.76 mmol/L for nonesterified fatty acids (NEFA, with 65% sensitivity and 92% specificity), more than 104 U/L for aspartate aminotransferase (AST, 74% and 85%, respectively), less than 140 U/L for cholinesterase (CHE, 75% and 59%, respectively), and more than 3.3 micromol/L for total bilirubin (TBIL, 58% and 83%, respectively). There were significant correlations between BHBA and glucose (R = -4.74), or CHE (R = -0.262), BHBA and NEFA (R = 0.520), or AST (R = 0.525), or TBIL (R = 0.278), or direct bilirubin (DBIL, R = 0.348).
CONCLUSIONS: AST, CHE, TBIL and NEFA may be useful parameters for risk prediction of ketosis. CLINICAL IMPORTANCE: This study might be of value in addressing novel directions for future research on the connection between ketosis and liver dysfunction.
ESTHER : Sun_2015_Vet.Q_35_159
PubMedSearch : Sun_2015_Vet.Q_35_159
PubMedID: 25831953

Title : A reference genome for common bean and genome-wide analysis of dual domestications - Schmutz_2014_Nat.Genet_46_707
Author(s) : Schmutz J , McClean PE , Mamidi S , Wu GA , Cannon SB , Grimwood J , Jenkins J , Shu S , Song Q , Chavarro C , Torres-Torres M , Geffroy V , Moghaddam SM , Gao D , Abernathy B , Barry K , Blair M , Brick MA , Chovatia M , Gepts P , Goodstein DM , Gonzales M , Hellsten U , Hyten DL , Jia G , Kelly JD , Kudrna D , Lee R , Richard MM , Miklas PN , Osorno JM , Rodrigues J , Thareau V , Urrea CA , Wang M , Yu Y , Zhang M , Wing RA , Cregan PB , Rokhsar DS , Jackson SA
Ref : Nat Genet , 46 :707 , 2014
Abstract : Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
ESTHER : Schmutz_2014_Nat.Genet_46_707
PubMedSearch : Schmutz_2014_Nat.Genet_46_707
PubMedID: 24908249
Gene_locus related to this paper: phavu-v7azs2 , phavu-v7awu7 , phavu-v7bpt6 , phavu-v7b6k3 , phavu-v7cry4

Title : Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing - Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
Author(s) : Hellsten U , Wright KM , Jenkins J , Shu S , Yuan Y , Wessler SR , Schmutz J , Willis JH , Rokhsar DS
Ref : Proc Natl Acad Sci U S A , 110 :19478 , 2013
Abstract : Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.
ESTHER : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedSearch : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedID: 24225854
Gene_locus related to this paper: erygu-a0a022qsc9 , erygu-a0a022qjb4 , erygu-a0a022px28 , erygu-a0a022rcn8 , erygu-a0a022r7z4 , erygu-a0a022rcp2 , erygu-a0a022r9s7 , erygu-a0a022put8 , erygu-a0a022r922 , erygu-a0a022qmg0 , erygu-a0a022rf01 , erygu-a0a022qnf5 , erygu-a0a022qs63 , erygu-a0a022rvn4 , erygu-a0a022rnw2 , erygu-a0a022s0h3 , erygu-a0a022qr26 , erygu-a0a022qi72 , erygu-a0a022qi30 , erygu-a0a022q165 , erygu-a0a022r728 , erygu-a0a022r7n8 , erygu-a0a022rm64 , erygu-a0a022s4c6 , erygu-a0a022rbl0 , erygu-a0a022rwi3 , erygu-a0a022rzg9

Title : The Reference Genome of the Halophytic Plant Eutrema salsugineum - Yang_2013_Front.Plant.Sci_4_46
Author(s) : Yang R , Jarvis DE , Chen H , Beilstein MA , Grimwood J , Jenkins J , Shu S , Prochnik S , Xin M , Ma C , Schmutz J , Wing RA , Mitchell-Olds T , Schumaker KS , Wang X
Ref : Front Plant Sci , 4 :46 , 2013
Abstract : Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8x coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.
ESTHER : Yang_2013_Front.Plant.Sci_4_46
PubMedSearch : Yang_2013_Front.Plant.Sci_4_46
PubMedID: 23518688
Gene_locus related to this paper: theha-e4mxu0 , thesl-v4nk72 , eutsa-v4l4z1 , eutsa-v4kk46 , eutsa-v4mej3 , eutsa-v4ns11 , eutsa-v4mg02 , eutsa-v4mqm9 , eutsa-v4k1y6 , eutsa-v4lad0 , eutsa-v4nr92 , eutsa-v4kqc3 , eutsa-v4l0s2 , eutsa-v4lip3 , eutsa-v4kkg2 , eutsa-v4kvd3 , eutsa-v4m9g4 , eutsa-v4lqg2 , eutsa-v4lp36 , eutsa-v4km66 , eutsa-v4nhr8 , eutsa-v4kqx9 , eutsa-v4lv73

Title : The Capsella rubella genome and the genomic consequences of rapid mating system evolution - Slotte_2013_Nat.Genet_45_831
Author(s) : Slotte T , Hazzouri KM , Agren JA , Koenig D , Maumus F , Guo YL , Steige K , Platts AE , Escobar JS , Newman LK , Wang W , Mandakova T , Vello E , Smith LM , Henz SR , Steffen J , Takuno S , Brandvain Y , Coop G , Andolfatto P , Hu TT , Blanchette M , Clark RM , Quesneville H , Nordborg M , Gaut BS , Lysak MA , Jenkins J , Grimwood J , Chapman J , Prochnik S , Shu S , Rokhsar D , Schmutz J , Weigel D , Wright SI
Ref : Nat Genet , 45 :831 , 2013
Abstract : The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
ESTHER : Slotte_2013_Nat.Genet_45_831
PubMedSearch : Slotte_2013_Nat.Genet_45_831
PubMedID: 23749190
Gene_locus related to this paper: arath-CGEP , 9bras-r0h1k6 , 9bras-r0gvg3 , 9bras-r0gv62 , 9bras-r0g5k5 , 9bras-r0f1u1 , 9bras-r0guy4 , 9bras-r0ien7 , 9bras-r0i2r7 , 9bras-r0fbh7 , 9bras-r0fnq1 , 9bras-r0hae6 , 9bras-r0gwt8 , 9bras-r0ewe4 , 9bras-r0gsz7 , 9bras-r0ij26 , 9bras-r0h783 , 9bras-r0i5w1 , 9bras-r0fgs3 , 9bras-r0h1e1 , 9bras-r0fme4 , 9bras-r0ieh8 , 9bras-r0f5l9 , 9bras-r0ffy6

Title : The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution - Verde_2013_Nat.Genet_45_487
Author(s) : Verde I , Abbott AG , Scalabrin S , Jung S , Shu S , Marroni F , Zhebentyayeva T , Dettori MT , Grimwood J , Cattonaro F , Zuccolo A , Rossini L , Jenkins J , Vendramin E , Meisel LA , Decroocq V , Sosinski B , Prochnik S , Mitros T , Policriti A , Cipriani G , Dondini L , Ficklin S , Goodstein DM , Xuan P , Del Fabbro C , Aramini V , Copetti D , Gonzalez S , Horner DS , Falchi R , Lucas S , Mica E , Maldonado J , Lazzari B , Bielenberg D , Pirona R , Miculan M , Barakat A , Testolin R , Stella A , Tartarini S , Tonutti P , Arus P , Orellana A , Wells C , Main D , Vizzotto G , Silva H , Salamini F , Schmutz J , Morgante M , Rokhsar DS
Ref : Nat Genet , 45 :487 , 2013
Abstract : Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
ESTHER : Verde_2013_Nat.Genet_45_487
PubMedSearch : Verde_2013_Nat.Genet_45_487
PubMedID: 23525075
Gene_locus related to this paper: prupe-a0a251pfr7 , prupe-a0a251r634 , prupe-m5x0p5 , prupe-m5xkg4 , prupe-m5x0q4 , prupe-m5vqa7 , prupe-m5wiw5 , prupe-a0a0u2wu32 , prupe-a0a251mtk1 , prupe-m5vl29 , prupe-m5vn82 , prupe-m5vq88 , prupe-m5y2s7 , prupe-m5wye7 , prupe-m5wxm4 , prupe-m5xqp6 , prupe-m5x4q4 , prupe-m5x4m1 , prupe-m5x6b3 , prupe-m5vlb6 , prupe-m5w4h3 , prupe-m5vlu4 , prupe-m5vln3 , prupe-a0a251myy7 , prupe-a0a251mws4 , prupe-m5vi18 , prupe-m5vh66 , prupe-m5xd54 , prupe-m5xqn2 , prupe-m5xr64 , prupe-m5vrm7 , prupe-m5vrk6 , prupe-m5vqp6 , prupe-a0a251nbb1 , prupe-a0a251nbd3 , prupe-a0a251nbb3 , prupe-a0a251nba0 , prupe-a0a251ndd4 , prupe-a0a251nbb6 , prupe-m5w315 , prupe-a0a251mwh1 , prupe-a0a251qn57 , prupe-m5vzh8 , prupe-m5xpz7 , prupe-m5xrp5 , prupe-m5wsr5 , prupe-m5xs20 , prupe-m5vl10 , prupe-a0a251nay9 , prupe-a0a251ndz1 , prupe-a0a251puf0 , prupe-m5wr61 , prupe-a0a251nyu6 , prupe-m5vl63

Title : Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres - Paterson_2012_Nature_492_423
Author(s) : Paterson AH , Wendel JF , Gundlach H , Guo H , Jenkins J , Jin D , Llewellyn D , Showmaker KC , Shu S , Udall J , Yoo MJ , Byers R , Chen W , Doron-Faigenboim A , Duke MV , Gong L , Grimwood J , Grover C , Grupp K , Hu G , Lee TH , Li J , Lin L , Liu T , Marler BS , Page JT , Roberts AW , Romanel E , Sanders WS , Szadkowski E , Tan X , Tang H , Xu C , Wang J , Wang Z , Zhang D , Zhang L , Ashrafi H , Bedon F , Bowers JE , Brubaker CL , Chee PW , Das S , Gingle AR , Haigler CH , Harker D , Hoffmann LV , Hovav R , Jones DC , Lemke C , Mansoor S , ur Rahman M , Rainville LN , Rambani A , Reddy UK , Rong JK , Saranga Y , Scheffler BE , Scheffler JA , Stelly DM , Triplett BA , Van Deynze A , Vaslin MF , Waghmare VN , Walford SA , Wright RJ , Zaki EA , Zhang T , Dennis ES , Mayer KF , Peterson DG , Rokhsar DS , Wang X , Schmutz J
Ref : Nature , 492 :423 , 2012
Abstract : Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
ESTHER : Paterson_2012_Nature_492_423
PubMedSearch : Paterson_2012_Nature_492_423
PubMedID: 23257886
Gene_locus related to this paper: gosra-a0a0d2qg22 , gosra-a0a0d2w3z1 , gosra-a0a0d2uuz7 , gosra-a0a0d2rxs2 , gosra-a0a0d2sdk0 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , gosra-a0a0d2vdc5 , gosra-a0a0d2vj24 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8kis4 , gosra-a0a0d2pul0 , gosra-a0a0d2p3f2 , gosra-a0a0d2ril5 , gosra-a0a0d2s7d5 , gosra-a0a0d2t9b3 , gosra-a0a0d2tw88 , gosra-a0a0d2umz5 , gosra-a0a0d2pzd7 , gosra-a0a0d2scu7 , gosra-a0a0d2vcx6

Title : The genome of the Western clawed frog Xenopus tropicalis - Hellsten_2010_Science_328_633
Author(s) : Hellsten U , Harland RM , Gilchrist MJ , Hendrix D , Jurka J , Kapitonov V , Ovcharenko I , Putnam NH , Shu S , Taher L , Blitz IL , Blumberg B , Dichmann DS , Dubchak I , Amaya E , Detter JC , Fletcher R , Gerhard DS , Goodstein D , Graves T , Grigoriev IV , Grimwood J , Kawashima T , Lindquist E , Lucas SM , Mead PE , Mitros T , Ogino H , Ohta Y , Poliakov AV , Pollet N , Robert J , Salamov A , Sater AK , Schmutz J , Terry A , Vize PD , Warren WC , Wells D , Wills A , Wilson RK , Zimmerman LB , Zorn AM , Grainger R , Grammer T , Khokha MK , Richardson PM , Rokhsar DS
Ref : Science , 328 :633 , 2010
Abstract : The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
ESTHER : Hellsten_2010_Science_328_633
PubMedSearch : Hellsten_2010_Science_328_633
PubMedID: 20431018
Gene_locus related to this paper: xenla-q6pcj9 , xentr-a9umk0 , xentr-abhdb , xentr-ACHE , xentr-b0bm77 , xentr-b1h0y7 , xentr-b2guc4 , xentr-b7zt03 , xentr-b7ztj4 , xentr-BCHE1 , xentr-BCHE2 , xentr-cxest2 , xentr-d2x2k4 , xentr-d2x2k6 , xentr-f6rff6 , xentr-f6v0g3 , xentr-f6v2j6 , xentr-f6v3z1 , xentr-f6y4c8 , xentr-f6yve5 , xentr-f7a4y9 , xentr-f7acc5 , xentr-f7e2e2 , xentr-LOC394897 , xentr-ndrg1 , xentr-q0vfb6 , xentr-f7cpl7 , xentr-f6yj44 , xentr-f7ejk4 , xentr-f6q8j8 , xentr-f6z8f0 , xentr-f7d709 , xentr-b0bmb8 , xentr-f7af63 , xentr-a0a1b8y2w9 , xentr-f7d4k9 , xentr-f6r032 , xentr-f6yvq3 , xentr-a0a1b8y2z3 , xentr-f7afg4 , xentr-f6xb15 , xentr-f7e1r2 , xentr-a4ihf1 , xentr-f7eue5 , xentr-f6u7u3 , xentr-f172a , xentr-f7equ8 , xentr-f7dd89 , xentr-a9jtx5

Title : The genome of Naegleria gruberi illuminates early eukaryotic versatility - Fritz-Laylin_2010_Cell_140_631
Author(s) : Fritz-Laylin LK , Prochnik SE , Ginger ML , Dacks JB , Carpenter ML , Field MC , Kuo A , Paredez A , Chapman J , Pham J , Shu S , Neupane R , Cipriano M , Mancuso J , Tu H , Salamov A , Lindquist E , Shapiro H , Lucas S , Grigoriev IV , Cande WZ , Fulton C , Rokhsar DS , Dawson SC
Ref : Cell , 140 :631 , 2010
Abstract : Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.
ESTHER : Fritz-Laylin_2010_Cell_140_631
PubMedSearch : Fritz-Laylin_2010_Cell_140_631
PubMedID: 20211133
Gene_locus related to this paper: naegr-d2ux86 , naegr-d2uyl7 , naegr-d2uyn1 , naegr-d2uzk6 , naegr-d2uzp4 , naegr-d2v1m1 , naegr-d2v3p5 , naegr-d2v5p1 , naegr-d2v6f6 , naegr-d2v6y9 , naegr-d2v8x8 , naegr-d2v186 , naegr-d2v339 , naegr-d2v556 , naegr-d2vbq7 , naegr-d2vdq6 , naegr-d2ve51 , naegr-d2vga2 , naegr-d2vgm9 , naegr-d2vh14 , naegr-d2vha2 , naegr-d2vj80 , naegr-d2vjj7 , naegr-d2vl41 , naegr-d2vmj5 , naegr-d2vms7 , naegr-d2vqi5 , naegr-d2vr44 , naegr-d2vrq2 , naegr-d2vs01 , naegr-d2vs58 , naegr-d2vts5 , naegr-d2vu69 , naegr-d2vvg8 , naegr-d2vxp2 , naegr-d2vyl1 , naegr-d2vzy5 , naegr-d2w0l5 , naegr-d2w0v9 , naegr-d2w3g8 , naegr-d2w3v7 , naegr-d2w3v8 , naegr-d2vct1

Title : The dynamic genome of Hydra - Chapman_2010_Nature_464_592
Author(s) : Chapman JA , Kirkness EF , Simakov O , Hampson SE , Mitros T , Weinmaier T , Rattei T , Balasubramanian PG , Borman J , Busam D , Disbennett K , Pfannkoch C , Sumin N , Sutton GG , Viswanathan LD , Walenz B , Goodstein DM , Hellsten U , Kawashima T , Prochnik SE , Putnam NH , Shu S , Blumberg B , Dana CE , Gee L , Kibler DF , Law L , Lindgens D , Martinez DE , Peng J , Wigge PA , Bertulat B , Guder C , Nakamura Y , Ozbek S , Watanabe H , Khalturin K , Hemmrich G , Franke A , Augustin R , Fraune S , Hayakawa E , Hayakawa S , Hirose M , Hwang JS , Ikeo K , Nishimiya-Fujisawa C , Ogura A , Takahashi T , Steinmetz PR , Zhang X , Aufschnaiter R , Eder MK , Gorny AK , Salvenmoser W , Heimberg AM , Wheeler BM , Peterson KJ , Bottger A , Tischler P , Wolf A , Gojobori T , Remington KA , Strausberg RL , Venter JC , Technau U , Hobmayer B , Bosch TC , Holstein TW , Fujisawa T , Bode HR , David CN , Rokhsar DS , Steele RE
Ref : Nature , 464 :592 , 2010
Abstract : The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
ESTHER : Chapman_2010_Nature_464_592
PubMedSearch : Chapman_2010_Nature_464_592
PubMedID: 20228792
Gene_locus related to this paper: 9burk-c9y6c0 , 9burk-c9y8q9 , 9burk-c9y9d4 , 9burk-c9ya28 , 9burk-c9yb37 , 9burk-c9ycr9 , 9burk-c9ydq0 , 9burk-c9ydr2 , 9burk-c9yew1 , 9burk-c9yf78 , 9burk-c9ygh2 , 9burk-c9y7j2

Title : Genome sequence of the palaeopolyploid soybean - Schmutz_2010_Nature_463_178
Author(s) : Schmutz J , Cannon SB , Schlueter J , Ma J , Mitros T , Nelson W , Hyten DL , Song Q , Thelen JJ , Cheng J , Xu D , Hellsten U , May GD , Yu Y , Sakurai T , Umezawa T , Bhattacharyya MK , Sandhu D , Valliyodan B , Lindquist E , Peto M , Grant D , Shu S , Goodstein D , Barry K , Futrell-Griggs M , Abernathy B , Du J , Tian Z , Zhu L , Gill N , Joshi T , Libault M , Sethuraman A , Zhang XC , Shinozaki K , Nguyen HT , Wing RA , Cregan P , Specht J , Grimwood J , Rokhsar D , Stacey G , Shoemaker RC , Jackson SA
Ref : Nature , 463 :178 , 2010
Abstract : Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
ESTHER : Schmutz_2010_Nature_463_178
PubMedSearch : Schmutz_2010_Nature_463_178
PubMedID: 20075913
Gene_locus related to this paper: soybn-c6t4m5 , soybn-c6t4p4 , soybn-c6tav4 , soybn-c6tdf9 , soybn-c6tiz7 , soybn-c6tmg3 , soybn-i1jgq5 , soybn-i1kpj2 , soybn-i1kwe7 , soybn-i1l7e3 , soybn-i1l497 , soybn-i1ll09 , soybn-i1lpi4 , soybn-i1jcw2 , soybn-i1jcw3 , soybn-i1jcw4 , soybn-i1jcw7 , soybn-i1k217 , soybn-i1kfz3 , soybn-i1lhi0 , soybn-k7k6s4 , soybn-i1jtw1 , soybn-c6tas4 , soybn-i1m910 , soybn-c6t7k8 , soybn-i1k636 , soybn-i1kju7 , soybn-i1j4c6 , soybn-i1lbk2 , soybn-i1jqy5 , soybn-i1nbj8 , soybn-i1j855 , soybn-i1l5a3 , soybn-k7mt28 , soybn-i1lau7 , soybn-i1lay0 , soybn-i1net3 , soybn-i1jr09 , soybn-i1ms08 , soybn-i1mmh5 , soybn-i1mly5 , soybn-i1mmh3 , soybn-i1mmh4 , soybn-i1ngu7 , soybn-k7ll20 , soybn-i1mly4 , soybn-a0a0r0i9y7 , soybn-a0a0r0j241 , soybn-i1les8 , soybn-k7n313 , soybn-i1kfj1 , soybn-a0a0r0k7x4 , soybn-i1ly30 , soybn-i1mwr8 , soybn-i1kfg5 , soybn-i1kly2 , soybn-a0a0r0ixi2 , soybn-i1jew0 , glyso-a0a445l5n1 , soybn-i1kfz9 , soybn-i1jqs1 , soybn-i1nbc7 , soybn-k7mm57 , soybn-a0a0r0fec7 , soybn-a0a0r0hcn9 , soybn-i1jx17 , soybn-k7kvv2 , soybn-i1kcl6 , soybn-i1kcl7 , soybn-i1jrc3 , soybn-i1nbz1 , soybn-a0a0r0euk2 , soybn-a0a0r0fx16 , soybn-a0a0r0k3t3 , soybn-i1kuc7 , soybn-i1lvy4

Title : The Release 5.1 annotation of Drosophila melanogaster heterochromatin - Smith_2007_Science_316_1586
Author(s) : Smith CD , Shu S , Mungall CJ , Karpen GH
Ref : Science , 316 :1586 , 2007
Abstract : The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.
ESTHER : Smith_2007_Science_316_1586
PubMedSearch : Smith_2007_Science_316_1586
PubMedID: 17569856
Gene_locus related to this paper: drome-CG9542 , drome-CG11309 , drome-KRAKEN , drome-nrtac