Xiang Jia Min

OrfPredictor: predicting protein-coding regions in EST-derived sequences

OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at .

Sequencing papaya X and Y h chromosomes reveals molecular basis of incipient sex chromosome evolution

Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Yh). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Yh chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Yh chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.

The pineapple genome and the evolution of CAM photosynthesis

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Effects of ammonium and inorganic carbon enrichment on growth and yield of a hydroponic tomato crop

Effects of varying the proportions of NO3— and NH4+ in the growth medium on seedling growth and tomato fruit yield (Lycopersicon esculentum L. cv. Trust F1) were investigated in greenhouse hydroponic experiments. The presence of NH4+ as the sole N source (11 mM) was toxic: it curtailed growth and decreased chlorophyll content of the leaves. However, at low concentration (10 % of total N), the presence of NH4+, with or without added dissolved inorganic carbon (DIC), increased vegetative growth and fruit yield by ˜ 15 %, and enhanced taste/flavor of the fruits. In DIC-enriched treatment, pH was maintained at 5.8 by addition of KHCO3 or as CaCO3. The presence of NH4+, at 10 % of total N, inhibited NO3— uptake rates by ˜ 27 %. The rates of uptake of NO3— and NH4+ were comparable (13.3 and 14.2 mmol plant—1 d—1, respectively, in the presence of DIC, and 14.7 and 14.0 mmol plant—1 d—1, respectively, in the absence of DIC), despite such a large difference in their concentrations in the nutrient feed solution. A higher proportion of NH4+ (up to 50 % of total N) had no further significant effect upon early vegetative growth, but in a long-term experiment resulted in a high incidence of blossom end-rot (BER) disease, thereby severely curtailing fruit yield. The presence of even 1.1 mM NH4+ reduced Ca2+ and Mg2+ accumulation in the leaves as well as in fruits. Einfluss von Ammonium und Zugaben von anorganischen Kohlenstoffverbindungen in einem Hydroponiksystem auf das Wachstum und den Fruchtertrag von Tomaten In Hydroponik-Gewachshaus-Versuchen wurden die Effekte eines variierten NO3—- und NH4+-Angebotes zu Tomaten (Lycopersicon esculentum L. cv. Trust F1) untersucht. Ein ausschliesliches Angebot von NH4+ (11 mM) wirkte toxisch, indem es das Wachstum hemmte und den Chlorophyllgehalt der Blatter absenkte. Bei geringerem Angebot jedoch (10 % NH4+ bei insgesamt 11 mM Gesamt-N) forderte NH4+ das vegetative Wachstum und den Fruchtertrag um 15 % und verbesserte ebenfalls den Geschmack der Fruchte gegenuber den Kontrollpflanzen, die nur mit Nitrat ernahrt worden waren. Diese Ertragssteigerung war unabhangig von der Zugabe an anorganischen Kohlenstoffverbindungen (DIC) zur Nahrlosung. In den DIC-angereicherten Versuchsgliedern wurde der pH der Nahrlosung mittels KHCO3 bzw. CaCO3 auf 5,8 konstant gehalten. Der 10 %ige NH4+-Anteil am Gesamt-N-Angebot senkte die Aufnahme von Nitrat um 27 %. Aber trotz des grosen Konzentrationsunterschiedes von NH4+ und NO3— in der NL waren die Aufnahmeraten fur NO3— und NH4+ mit 13,3 und 14,2 mmol Pfl.—1 Tag—1 (+ DIC) und 14,7 bzw. 14,0 mmol Pfl.—1 Tag—1 (— DIC) gleich. Eine Steigerung des NH4+-Anteils in der NL (bis zu 50 %) hatte keine zusatzlichen signifikanten Effekte auf das fruhe vegetative Wachstum, bewirkte jedoch Fruchtendfaule, weshalb der Fruchtertrag abfiel. Bereits das NH4+ Angebot von 1,1 mM NH4+ in der NL reduzierte die Ca2+- und Mg2+-Akkumulation in Blattern und Fruchten.

Assessing the effect of varying sequence length on DNA barcoding of fungi.

DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences — of various lengths — and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (∼600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi.

FunSecKB: the Fungal Secretome KnowledgeBase

The Fungal Secretome KnowledgeBase (FunSecKB) provides a resource of secreted fungal proteins, i.e. secretomes, identified from all available fungal protein data in the NCBI RefSeq database. The secreted proteins were identified using a well evaluated computational protocol which includes SignalP, WolfPsort and Phobius for signal peptide or subcellular location prediction, TMHMM for identifying membrane proteins, and PS-Scan for identifying endoplasmic reticulum (ER) target proteins. The entries were mapped to the UniProt database and any annotations of subcellular locations that were either manually curated or computationally predicted were included in FunSecKB. Using a web-based user interface, the database is searchable, browsable and downloadable by using NCBI’s RefSeq accession or gi number, UniProt accession number, keyword or by species. A BLAST utility was integrated to allow users to query the database by sequence similarity. A user submission tool was implemented to support community annotation of subcellular locations of fungal proteins. With the complete fungal data from RefSeq and associated web-based tools, FunSecKB will be a valuable resource for exploring the potential applications of fungal secreted proteins. Database URL: http://proteomics.ysu.edu/secretomes/fungi.php

Genome-Wide Landscape of Alternative Splicing Events in Brachypodium distachyon

Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%). We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The ‘complex event’ that consists of a combination of two or more basic splicing events accounted for ∼14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).

Generation, annotation, and analysis of an extensive Aspergillus niger EST collection

BackgroundAspergillus niger, a saprophyte commonly found on decaying vegetation, is widely used and studied for industrial purposes. Despite its place as one of the most important organisms for commercial applications, the lack of available information about its genetic makeup limits research with this filamentous fungus.ResultsWe present here the analysis of 12,820 expressed sequence tags (ESTs) generated from A. niger cultured under seven different growth conditions. These ESTs identify about 5,108 genes of which 44.5% code for proteins sharing similarity (E ≤ 1e -5) with GenBank entries of known function, 38% code for proteins that only share similarity with GenBank entries of unknown function and 17.5% encode proteins that do not have a GenBank homolog. Using the Gene Ontology hierarchy, we present a first classification of the A. niger proteins encoded by these genes and compare its protein repertoire with other well-studied fungal species. We have established a searchable web-based database that includes the EST and derived contig sequences and their annotation. Details about this project and access to the annotated A. niger database are available.ConclusionThis EST collection and its annotation provide a significant resource for fundamental and applied research with A. niger. The gene set identified in this manuscript will be highly useful in the annotation of the genome sequence of A. niger, the genes described in the manuscript, especially those encoding hydrolytic enzymes will provide a valuable source for researchers interested in enzyme properties and applications.

TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences

TargetIdentifier is a webserver that identifies full-length cDNA sequences from the expressed sequence tag (EST)-derived contig and singleton data. To accomplish this TargetIdentifier uses BLASTX alignments as a guide to locate protein coding regions and potential start and stop codons. This information is then used to determine whether the EST-derived sequences include their translation start codons. The algorithm also uses the BLASTX output to assign putative functions to the query sequences. The server is available at .

DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition

DNA barcodes have achieved prominence as a tool for species-level identifications. Consequently, there is a rapidly growing database of these short sequences from a wide variety of taxa. In this study, we have analyzed the correlation between the nucleotide content of the short DNA barcode sequences and the genomes from which they are derived. Our results show that such short sequences can yield important, and surprisingly accurate, information about the composition of the entire genome. In other words, for unsequenced genomes, the DNA barcodes can provide a quick preview of the whole genome composition.