Transcriptome of Xenopus andrei, an octoploid frog, during embryonic development.
ABSTRACT: Although polyploidy occurs throughout the fish and amphibian lineages, the Xenopus genus exhibits a high incidence of polyploidy, with 25 out of the 26 known species being polyploid. However, transcriptomic information is currently available for only one of these species, the tetraploid Xenopus laevis. Xenopus andrei, an octoploid species within the Xenopus genus, offers an opportunity for assessing a novel polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281). Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639). To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome. In total, 849?Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases. This RNA-Seq and transcriptome data will be valuable for comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication and polyploidy in vertebrates.
Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates. Overall design: Embryos were obtained from one mating of two adult X. andrei frogs. Nine samples are analyzed, each from a different developmental stage.
Project description:Blueberry is an economically important berry crop. Both production and consumption of blueberries have increased sharply worldwide in recent years at least partly due to their known health benefits. The development of improved genomic resources for blueberry, such as a well-assembled genome and transcriptome, could accelerate breeding through genomic-assisted approaches. To enrich available transcriptome data and identify genes potentially involved in fruit quality, RNA sequencing was performed on fruit tissue from two northern-adapted hybrid blueberry breeding populations. RNA-seq was carried out using the Illumina HiSeqTM 2500 platform. Because of the absence of a reference-grade genome for blueberry, a transcriptome was de novo assembled from this RNA-seq data and other publicly available transcriptome data from blueberry downloaded from the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) using Trinity. After removing redundancy, this resulted in a dataset of 91,861 blueberry unigenes. This unigene dataset was functionally annotated using the NCBI-Nr protein database. All raw reads from the breeding populations were deposited in the NCBI SRA with accession numbers SRR6281886, SRR6281887, SRR6281888, and SRR6281889. The de novo transcriptome assembly was deposited at NCBI Transcriptome Shotgun Assembly (TSA) database with accession number GGAB00000000. These data will provide real expression evidence for the blueberry genome gene prediction and gene functional annotation and a reference transcriptome for future gene expression studies involving blueberry fruit.
Project description:Strawberry (Fragaria x ananassa) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry (Fragaria x ananassa). Here, we used long-read sequencing (LRS) technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry. We obtained a reference transcriptome with 119,897 unique full-length isoforms, including 2017 new isoforms and 2510 long noncoding RNAs. Based on the genome of the plausible progenitor (Fragaria vesca), 20,229 alternative splicing (AS) events were identified. Using this transcriptome, we found 17,485 differentially expressed transcripts during strawberry fruit development, including 527 transcription factors (TFs) belonging to 41 families. The expression profiles of all members of the auxin, ABA pathway, and anthocyanin biosynthesis gene families were also examined, and many of them were highly expressed at the ripe fruit stage, strongly indicating that the role of those genes is in the regulation of fruit ripening. We produce a high-quality reference transcriptome for octoploid strawberry, including much of the full-length transcript diversity, to help understand the regulatory mechanisms of fruit development and maturation of polyploid species, particularly via elucidation of the biochemical pathways involved in auxin, ABA, and anthocyanin biosynthesis.
Project description:We performed RNA sequencing (RNA-Seq) at ten successive developmental stages in embryos of the common house spider Parasteatoda tepidariorum. Two independent datasets from two pairs of parents represent the normalized coverage of mapped RNA-Seq reads along scaffolds of the P. tepidariorum genome assembly. Transcript abundance was calculated against existing AUGUSTUS gene models. The datasets have been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession number GSE112712.
Project description:Polyploidy in Rhododendron fortunei has great potential to improve its horticultural and commercial value, and to also meet market demands. In this study, a feasible method for polyploid induction in R. fortunei via colchicine treatment was established, and the obtained polyploid plants were identified and characterized. As a result, the stem bases of tissue-cultured plantlets treated with 0.1% colchicine for 24 h showed the highest polyploid induction with a rate of 36.67%. By flow cytometric analysis, 69 tetraploids and 29 octoploids were identified in the regenerated plants that were examined. Phenotypic analysis indicated that the leaves of tetraploid and octoploid plants were smaller, rounder and thicker with more abundant and longer epidermal hairs than those of diploids. Furthermore, the stomata of polyploids were larger and sparser than those of diploids. An increase in chlorophyll content was also detected in polyploids, which resulted in darker green leaves. In conclusion, our study established an effective method to induce polyploidy in R. fortunei, which could be used to develop new genetic resources for breeding R. fortunei and other Rhododendron species in the future.
Project description:Polyploidization contributes to the complexity of gene expression, resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of the tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short-read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors. Caffeine and sucrose genes were targeted for case analysis. An isoform-level tetraploid coffee bean reference transcriptome with 95 995 distinct transcripts (average 3236 bp) was obtained. A total of 88 715 sequences (92.42%) were annotated with BLASTx against NCBI non-redundant plant proteins, including 34 719 high-quality annotations. Further BLASTn analysis against NCBI non-redundant nucleotide sequences, Coffea canephora coding sequences with UTR, C. arabica ESTs, and Rfam resulted in 1213 sequences without hits, were potential novel genes in coffee. Longer UTRs were captured, especially in the 5?UTRs, facilitating the identification of upstream open reading frames. The LRS also revealed more and longer transcript variants in key caffeine and sucrose metabolism genes from this polyploid genome. Long sequences (>10 kilo base) were poorly annotated. LRS technology shows the limitation of previous studies. It provides an important tool to produce a reference transcriptome including more of the diversity of full-length transcripts to help understand the biology and support the genetic improvement of polyploid species such as coffee.
Project description:Recently, using the frog Xenopus laevis as a model system, we showed that transcription factor Rfx2 coordinates many genes involved in ciliogenesis and cell movement in multiciliated cells (Chung et al., 2014). To our knowledge, it was the first paper to utilize the genomic resources, including genome sequences and interim gene annotations, from the ongoing Xenopus laevis genome project. For researchers who are interested in the application of genomics and systems biology approaches in Xenopus studies, here we provide additional details about our dataset (NCBI GEO accession number GSE50593) and describe how we analyzed RNA-seq and ChIP-seq data to identify direct targets of Rfx2.
Project description:Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.
Project description:Polyploidy is a fundamental process in plant evolution. Understanding the polyploidy-associated effects on plant reproduction is essential for polyploid breeding program. In the present study, our cytological analysis firstly demonstrated that an overall course of meiosis was apparently distorted in the synthetic polyploid Brassica rapa in comparison with its diploid progenitor. To elucidate genetic basis of this irregular meiosis at a molecular level, the comparative RNA-seq analysis was further used to investigate differential genetic regulation of developing floral buds identified at meiosis between autotetraploid and diploid B. rapa. In total, compared to its diploid counterparts, among all 40,927 expressed genes revealed, 4,601 differentially expressed genes (DEGs) were identified in the floral buds of autotetraploid B. rapa, among which 288 DEGs annotated were involved in meiosis. Notably, DMC1 identified as one previously known meiosis-specific gene involved in inter-homologous chromosome dependent repair of DNA double stranded breaks (DSBs), was significantly down-regulated in autotetraploid B. rapa, which presumably contributed to abnormal progression during meiosis I. Although certain DEGs associated with RNA helicase, cell cycling, and somatic DNA repair were up-regulated after genome duplication, genes associated with meiotic DSB repair were significantly down-regulated. Furthermore, the expression of randomly selected DEGs by RNA-seq analysis was confirmed by quantitative real-time PCR analysis in both B. rapa and Arabidopsis thaliana. Our results firstly account for adverse effects of polyploidy on an entire course of meiosis at both cytological and transcriptomic levels, and allow for a comprehensive understanding of the uniformity and differences in the transcriptome of floral buds at meiosis between diploid and polyploid B. rapa as well.
Project description:Ganoderma boninense is known to be the causal agent for basal stem rot (BSR) affecting the oil palm industry worldwide thus cumulating to high economic losses every year. Several reports have shown that a compatible monokaryon pair needs to mate; producing dikaryotic mycelia to initiate the infection towards the oil palm. However, the molecular events occurs during mating process are not well understood. We performed transcriptome sequencing using Illumina RNA-seq technology and de novo assembly of the transcripts from monokaryon, mating junction and dikaryon mycelia of G. boninense. Raw reads from these three libraries were deposited in the NCBI database with accession number SRR1745787, SRR1745773 and SRR1745777, respectively.