A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Background

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models.

Results

A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models.

Conclusions

Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4656-3) contains supplementary material, which is available to authorized users.

Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al.

METHOD

some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS). By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS) method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145) of BamH I sites shared with the reference genome, compared to only 14% (11,513) by stdGBS.

An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes

Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.

[Coronary revascularization with extracorporeal circulation, aortic clamping or OPCAB: does the method's choice influence the results?]

BACKGROUND AND OBJECTIVES

Off pump CABG-OPCAB is the most recent development in coronary surgery and is aimed to avoid the complications of extracorporeal circulation and to compete with interventional cardiology. The objective of this study is to compare 3 methods for cardiac support for CABG.

METHODS

Between February 2001 and December 2002 ninety consecutive patients were operated by the same surgeon and the same team with the following techniques: extracorporeal circulation (CEC) and ischaemic arrest, CEC and beating heart, and OPCAB.

RESULTS

There were no difference in mortality and morbidity for the 3 groups of patients. The OPCAB group showed less ventilation time, less blood transfusion needs and shorter hospital stays than the other 2 groups of patients that showed no differences between each other.

CONCLUSION

OPCAB is safe and showed slight advantage over CEC supported groups but the number of grafts per patient was smaller.

A fluorescence energy transfer method for analyzing protein oligomeric structure: application to phospholamban

We have developed a method using fluorescence energy transfer (FET) to analyze protein oligomeric structure. Two populations of a protein are labeled with fluorescent donor and acceptor, respectively, then mixed at a defined donor/acceptor ratio. A theoretical simulation, assuming random mixing and association among protein subunits in a ring-shaped homo-oligomer, was used to determine the dependence of FET on the number of subunits, the distance between labeled sites on different subunits, and the fraction of subunits remaining monomeric. By measuring FET as a function of the donor/acceptor ratio, the above parameters of the oligomeric structure can be resolved over a substantial range of their values. We used this approach to investigate the oligomeric structure of phospholamban (PLB), a 52-amino acid protein in cardiac sarcoplasmic reticulum (SR). Phosphorylation of PLB regulates the SR Ca-ATPase. Because PLB exists primarily as a homopentamer on sodium dodecyl sulfate polyacrylamide gel electrophoresis, it has been proposed that the pentameric structure of PLB is important for its regulatory function. However, this hypothesis must be tested by determining directly the oligomeric structure of PLB in the lipid membrane. To accomplish this goal, PLB was labeled at Lys-3 in the cytoplasmic domain, with two different amine-reactive donor/acceptor pairs, which gave very similar FET results. In detergent solutions, FET was not observed unless the sample was first boiled to facilitate subunit mixing. In lipid bilayers, FET was observed at 25 degrees C without boiling, indicating a dynamic equilibrium among PLB subunits in the membrane. Analysis of the FET data indicated that the dye-labeled PLB is predominantly in oligomers having at least 8 subunits, that 7-23% of the PLB subunits are monomeric, and that the distance between dyes on adjacent PLB subunits is about 10 A. A point mutation of PLB (L37A) that runs as monomer on SDS-PAGE showed no energy transfer, confirming its monomeric state in the membrane. We conclude that FET is a powerful approach for analyzing the oligomeric structure of PLB, and this method is applicable to other oligomeric proteins.

Tryptophan dynamics of the FK506 binding protein: time-resolved fluorescence and simulations

The FK506-binding protein (FKBP12) is important in the immunosuppressant action of FK506 and rapamycin. We have investigated Trp side chain dynamics in FKBP12, with and without a bound immunosuppressant, by measuring the Trp time-resolved fluorescence anisotropy decay r(t). The r(t) for W59 in aqueous uncomplexed FKBP12 at 20 degrees C is well described by a single exponential with a recovered initial anisotropy, r(eff)o, of 0.192 and an overall rotational correlation time for the protein, phi p, of 4.7 ns; r(eff)o = 0.214 and phi p = 4.2 ns for the FKBP12/FK506 complex. Using an expression for the order parameter squared, namely S2 = r(eff)o/rTo, where rTo is the vitrified steady-state excitation anisotropy, we recovered an S2 of 0.75 for W59 fluorescence in uncomplexed FKBP12 and S2 approximately equal to 1 in the FKBP12/FK506 complex. Results obtained for the FKBP12/rapamycin complex are similar to those found for the FKBP12/FK506 complex. Minimum perturbation mapping simulations were performed on the free and complexed forms of FKBP12 and the results were generally in agreement with the experimental data.

In vitro inhibition of marginal caries-like lesions with fluoride-containing amalgam

Carious lesions surrounding restorations represent one of the main causes of restoration failure. The addition of fluoride compounds to dental restorative materials prevents or reduces recurrent caries. The purpose of this study was to compare the capacity of three restorative materials to inhibit the development of recurrent caries in vitro. Thirty unrestored, noncarious premolars that were being extracted for orthodontic reasons were sectioned in half buccolingually and divided into three groups. One of the groups was restored with conventional amalgam. The second group was restored with a fluoride-containing amalgam, and the third group was restored with a glass-ionomer cement. All the samples were submitted to a medium containing Streptococcus mutans (Ingbritt strain) for 8 weeks. At the end of the 8-week incubation period, the samples were cut into 100 microns sections, soaked in Quinoline (IR = 1.62), and observed with light transmission and polarized light microscopy. The development of artificial caries in the cavity walls was measured in microns. The results show that conventional amalgam had an average caries penetration of 160 microns, fluoride-containing amalgam 46 microns, and glass-ionomer cement 11 microns. Glass-ionomer cement gave the best protection against recurrent caries.

[Breast cancer in the pregnancy-puerperal cycle]

From 1978 to 1988, 611 cases of breast cancer were seen by the Mastology Department of the Beneficência Portuguesa Hospital in São Paulo, Brazil. Thirteen (2.12%) cases were associated to pregnancy, and nine (2.4%) became pregnant after treatment. The patients were submitted to surgery and the authors waited till the end of pregnancy to perform the Rt and/or Qt. Two cases could not be submitted to any kind of treatment. Whenever tests indicated fetal maturity, the option was to perform a caesarean section, and oophorectomy was performed in the most advanced cases. Among patients who became pregnant after treatment, initial cases were predominant and their pregnancies went to term with no problem. The authors compare their results to data found in literature and draw attention to anticonception in mastectomized patients.

[Microbiological study of salt (sodium chloride) of marine origin]

Foram analisadas 19 amostras de SAL (NaCl), tipo grosso, oriundas de diferentes salinas, para verificação da flora microbiana e presença de bactérias nocivas em Microbiologia Alimentar. O material apresentou grande contaminação por microrganismos saprófitas, bactérias aeróbias e anaeróbias, Gram positivas e negativas, proteolíticas, pigmentadas, esporuladas, leveduras e fungos. A alta incidência das bactérias halofílicas "vermelhas", responsáveis pela deterioração de carnes, pescados e outros produtos salgados foi estudada. A freqüência, em 15 amostras de SAL, de bactérias esporuladas termorresistentes foi calculada em 33%, possuindo um SAL germe termofílico. Para anaeróbios a positividade foi de 80%, havendo esporulação em 40% das culturas isoladas. Os índices para leveduras e fungos foram de 73% e 93%, respectivamente.