Understanding the genetic underpinnings of plant and animal functions

Most Recent Agrigenomics Publications

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.

Wang Y, Lu Y, Zhang Y, Ning Z, Li Y, Zhao Q, Lu H, Huang R, Xia X, Feng Q, Liang X, Liu K, Zhang L, Lu T, Huang T, Fan D, Weng Q, Zhu C, Lu Y, Li W, Wen Z, Zhou C, Tian Q, Kang X, Shi M, Zhang W, Jang S, Du F, He S, Liao L, Li Y, Gui B, He H, Ning Z, Yang C, He L, Luo L, Yang R, Luo Q, Liu X, Li S, Huang W, Xiao L, Lin H, Han B, Zhu Z

Nat Genet 47
625-31

2015

Abstract Illumina Summary

Abstract

The grass carp is an important farmed fish, accounting for ~16% of global freshwater aquaculture, and has a vegetarian diet. Here we report a 0.9-Gb draft genome of a gynogenetic female adult and a 1.07-Gb genome of a wild male adult. Genome annotation identified 27,263 protein-coding gene models in the female genome. A total of 114 scaffolds consisting of 573 Mb are anchored on 24 linkage groups. Divergence between grass carp and zebrafish is estimated to have occurred 49-54 million years ago. We identify a chromosome fusion in grass carp relative to zebrafish and report frequent crossovers between the grass carp X and Y chromosomes. We find that transcriptional activation of the mevalonate pathway and steroid biosynthesis in liver is associated with the grass carp's adaptation from a carnivorous to an herbivorous diet. We believe that the grass carp genome could serve as an initial platform for breeding better-quality fish using a genomic approach.

Illumina Summary

The grass carp is an important farmed fish, accounting for ~16% of global freshwater aquaculture. This paper presents a 0.9-Gb draft genome of a gynogenetic female adult and a 1.07-Gb genome of a wild male adult grass carp. The authors used Illumina high-throughput sequencing on HiSeq 2000 to sequence the carp DNA collected from wild grass carp and analysed the two assembled genomes to annotate protein-coding genes and to compare to other species in the carp evolutionary history. The phylogenetic analysis highlighted that transcriptional activation of the mevalonate pathway and steroid biosynthesis in the carp liver is associated with the grass carp's adaptation from a carnivorous to an herbivorous diet.

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L

Nature 518
371-5

2015

Abstract Illumina Summary

Abstract

Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.

Illumina Summary

Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. This study set out to evaluate the phylogeny of Galapagos finches, not by phenotypic features as initiated by Darwin, but with whole-genome sequencing on Illumina HiSeq. The resulting phylogeny based on autosomal genome sequences diverged on several species from that of Darwins phenotypic phylogeny. The authors used genome comparison of windows of 15kb between two closely related species with distinct beak shapes to identify loci associated with beak shapes. This approach revealed a 240kb haplotype encompassing the ALX1 gene that encodes a transcription factor affection craniofacial development.

Specialized insulin is used for chemical warfare by fish-hunting cone snails.

Safavi-Hemami H, Gajewiak J, Karanth S, Robinson SD, Ueberheide B, Douglass AD, Schlegel A, Imperial JS, Watkins M, Bandyopadhyay PK, Yandell M, Li Q, Purcell AW, Norton RS, Ellgaard L, Olivera BM

Proc Natl
Acad Sci U S
A 112 1743-8

2015

Abstract Illumina Summary

Abstract

More than 100 species of venomous cone snails (genus Conus) are highly effective predators of fish. The vast majority of venom components identified and functionally characterized to date are neurotoxins specifically targeted to receptors, ion channels, and transporters in the nervous system of prey, predators, or competitors. Here we describe a venom component targeting energy metabolism, a radically different mechanism. Two fish-hunting cone snails, Conus geographus and Conus tulipa, have evolved specialized insulins that are expressed as major components of their venoms. These insulins are distinctive in having much greater similarity to fish insulins than to the molluscan hormone and are unique in that posttranslational modifications characteristic of conotoxins (hydroxyproline, ?-carboxyglutamate) are present. When injected into fish, the venom insulin elicits hypoglycemic shock, a condition characterized by dangerously low blood glucose. Our evidence suggests that insulin is specifically used as a weapon for prey capture by a subset of fish-hunting cone snails that use a net strategy to capture prey. Insulin appears to be a component of the nirvana cabal, a toxin combination in these venoms that is released into the water to disorient schools of small fish, making them easier to engulf with the snail's distended false mouth, which functions as a net. If an entire school of fish simultaneously experiences hypoglycemic shock, this should directly facilitate capture by the predatory snail.

Illumina Summary

Venomous cone snails (genus Conus) are highly effective predators of fish. The snails are known to use conotoxins in their venom, targeting the fish nervous system. In this study, the authors describe two fish-hunting cone snails that target the fish energy metabolism via a specialized insulin as a major component of their venoms. The venom insulin elicits hypoglycemic shock, a condition characterized by dangerously low blood glucose. The authors identified the venom component via mass spectrometry and characterized its expression via Illumina RNA sequencing.

The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ

Nat Genet

2014

Abstract Illumina Summary

Abstract

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

Illumina Summary

The orchid family, orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. This study presents the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. The authors used Illumina HiSeq 2000 for high throughput sequencing of libraries of insert sizes varying from 160bp to 20kb. The genome was annotated for gene content and evaluated in a phylogenetic analysis to characterize the evolutionary history of the crassulacean acid metabolism (CAM) genes.

Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior.

Li Q, Wang Z, Lian J, Schiøtt M, Jin L, Zhang P, Zhang Y, Nygaard S, Peng Z, Zhou Y, Deng Y, Zhang W, Boomsma JJ, Zhang G

Nat Commun
5 4943

2014

Abstract Illumina Summary

Abstract

Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8-23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants.

Illumina Summary

Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. In this study, the authors used strand-specific RNA-Seq on Illumina HiSeq2000 on head tissue samples of the female castes of A. echinatior and data from other genome-sequenced ants to evaluate the possible role of RNA editing in modulating functional gene differentiation among castes. They found the editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most editing sites were found to be species-specific, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants. and show that RNA editing may be an important but underappreciated mechanism that shapes caste behaviour in ants.

Genomic analyses provide insights into the history of tomato breeding.

Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S

Nat Genet 46
1220-6

2014

Abstract Illumina Summary

Abstract

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ~100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

Illumina Summary

The histories of crop domestication and breeding are recorded in genomes. This study report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions from the Tomato Genetics Resource Center. The authors used Illumina HiSeq 2000 for DNA sequencing and analysed the single nucleotide polymorphisms with a focus on two independent sets of quantitative trait loci (QTLs). The authors discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions.

Abstract Illumina Summary

Abstract

The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), are two closely related and sympatric pests of coniferous forests in southwestern China, and olfactory communication systems of these two insects have received considerable attention because of their economic importance. However, there is little information on the molecular aspect of odor detection about these insects. Furthermore, although lepidopteran species have been widely used in studies of insect olfaction, few work made comparison between sister moths on the olfactory recognition mechanisms. In this study, next-generation sequencing of the antennal transcriptome of these two moths were performed to identify the major olfactory genes. After comparing the antennal transcriptome of these two moths, we found that they exhibit highly similar transcripts-associated GO terms. Chemosensory gene families were further analyzed in both species. We identified 23 putative odorant binding proteins (OBP), 17 chemosensory proteins (CSP), two sensory neuron membrane proteins (SNMP), 33 odorant receptors (OR), and 10 ionotropic receptors (IR) in D. houi; and 27 putative OBPs, 17 CSPs, two SNMPs, 33 ORs, and nine IRs in D. kikuchii. All these transcripts were full-length or almost full-length. The predicted protein sequences were compared with orthologs in other species of Lepidoptera and model insects, including Bombyx mori, Manduca sexta, Heliothis virescens, Danaus plexippus, Sesamia inferens, Cydia pomonella, and Drosophila melanogaster. The sequence homologies of the orthologous genes in D. houi and D. kikuchii are very high. Furthermore, the olfactory genes were classed according to their expression level, and the highly expressed genes are our target for further function investigation. Interestingly, many highly expressed genes are ortholog gene of D. houi and D. kikuchii. We also found that the Classic OBPs were further separated into three groups according to their motifs, which will help future functional researches. Surprisingly, no pheromone receptor was identified in the two Dendrolimus species, which may indicate a special pheromone identification mechanism in Dendrolimus. Our work allows for further functional studies of pheromones and host volatile recognition genes, and give novel candidate targets for pest management.

Illumina Summary

The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), are two closely related and sympatric pests of coniferous forests in southwestern China, and olfactory communication systems of these two insects have received considerable attention because of their economic importance. In this paper, the authors used Illumina sequencing on HiSeq2000 to perform a comprehensive analysis of the antennal transcriptomes of these two sympatric forest moths. The improved understanding of the molecular pathways and function of the moth olfactory receptors will provide new targets for pest managment in the future.

Abstract Illumina Summary

Abstract

Although various elements of the olfactory system have been elucidated in insects, it remains practically unstudied in crustaceans at a molecular level. Among crustaceans, some species are classified as ectoparasites that impact the finfish aquaculture industry. Thus, there is an urgent need to identify and comprehend the signaling pathways used by these in host recognition. The present study, through RNA-seq and qPCR analyses, found novel transcripts involved in the olfactory system of Caligus rogercresseyi, in addition to the transcriptomic patterns expressed during different stages of salmon lice development. From a transcriptomic library generated by Illumina sequencing, contigs that annotated for ionotropic receptors and other genes implicated in the olfactory system were identified and extracted. Full length mRNA was obtained for the ionotropic glutamate receptor 25, which had 3923bp, and for the glutamate receptor ionotropic kainate 2, which had 2737bp. Furthermore, two other transcripts identified as glutamate receptor, ionotropic kainate 2-like were found. In silico analysis was performed for the transcription expression from different stages of development in C. rogercresseyi, and clusters according to RPKM values were constructed. Gene transcription data were validated through qPCR assays in ionotropic receptors, and showed an expression of glutamate receptor 25 associated with the copepodid stage whereas adults, especially male adults, were associated with the kainate 2 and kainate 2-like transcripts. Additionally, gene transcription analysis of the ionotropic receptors showed an overexpression in response to the presence of masking compounds and immunostimulant in salmon diets. This response correlated to a reduction in sea lice infection following in vivo challenge. Diets with masking compounds showed a decrease of lice infestation of up to 25%. This work contributes to the available knowledge on chemosensory systems in this ectoparasite, providing novel elements towards understanding the host-finding process of the salmon louse C. rogercresseyi.

Illumina Summary

Among crustaceans, some species are classified as ectoparasites that impact the finfish aquaculture industry. Some species are known to locate their host using various mechanism, including recognition of semiochemicals. In this study, the authors studied the olfactory system of Caligus rogercresseyi using transcriptomics analysis using the Illumina MiSeq platform. The ionotropic receptors showed an overexpression in response to the presence of masking compounds and immunostimulant in salmon diets. This response correlated to a reduction in sea lice infection following in vivo challenge: Diets with masking compounds showed a decrease of lice infestation of up to 25%.

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z

Sci Rep 4
4519

2014

Abstract Illumina Summary

Abstract

RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.

Illumina Summary

The Zea Maiys (maize) genome presents a good model for a plant transcriptomic study as there are many challenges associated with gene identification and annotation. The goal of this study was to explore the impact of read depth on the comprehensiveness of assembly and and annotation by sequencing the transcriptome of a maize seedling mRNA sample. The sample was sequenced using a combination of Illumina Genome Analyzer and Illumina HiSeq. A total of 126,708 transcripts were detected from the nearly 3 billion RNA-Seq reads. Current annotation was improved by adding 4,842 previously unannotated transcript variants to the maize genome and the authors demonstrated the power of deep sequencing for detecting rare transcripts.

Legume genomics: understanding biology through DNA and RNA sequencing.

O'Rourke JA, Bolon YT, Bucciarelli B, Vance CP

Ann Bot 113
1107-20

2014

Abstract

Abstract

The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication.

Illumina Summary

Single-cell genomics and single-cell transcriptomics have emerged as powerful tools to study the biology of single cells at a genome-wide scale. In this breakthrough paper, the authors demonstrate how they extracted both DNA and mRNA from the same cell to perform complete transcriptome and genome analysis. Using a quasilinear amplification strategy and Illumina HiSeq for sequencing, they show that the efficiency of their approach is similar to existing methods for single-cell sequencing of either genomic DNA or mRNA. In addition, they found that genes with high cell-to-cell variability in transcript numbers generally have lower genomic copy numbers, and vice versa.

Abstract Illumina Summary

Abstract

MicroRNAs (miRNA) play a critical role in post-transcriptional regulation by influencing the 3'-UTR of target genes. Using two inbred White Leghorn chicken lines, line 6.3 and line 7.2 showing Marek's disease-resistant and -susceptible phenotypes, respectively, we used small RNA high-throughput sequencing (HTS) to investigate whether miRNAs are differently expressed in these two chicken lines after inducing necrotic enteritis (NE). The 12 miRNAs, selected from the most down-regulated or up-regulated miRNAs following NE induction, were confirmed by their expressions in real-time PCR. Among these miRNAs, miR-215, miR-217, miR-194, miR-200a, miR-200b, miR-216a, miR-216b, and miR-429 were highly expressed in intestine derived from line 7.2, whereas, miR-1782 and miR-499 were down-regulated. In spleen, miR-34b and miR-1684 were the most up-regulated miRNAs in line 6.3. Notably, five out of six target genes, CXCR5, BCL2, GJA1, TCF12, and TAB3 were differentially expressed between line 6.3 and line 7.2, and showed suppression in the MD-susceptible chicken line. Their expression levels were conversely correlated with those of miRNA obtained from both HTS and quantitative real-time PCR. These results suggest that some miRNAs are differentially altered in response to NE and they modulate the expression of their target genes in the two inbred lines. Collectively, HTS analysis of intestinal miRNAs from NE-afflicted inbred chickens showing different disease phenotypes led to the identification of host immunity genes regulated by miRNA. Future studies of the function of these miRNAs and their target genes in the host will lead to enhanced understanding of molecular mechanisms controlling host-pathogen interaction in NE.

Illumina Summary

Necrotis enteritis (NE) is a major enteric disease of poultry caused by infection with C. perfringens. This study examined the NE disease progression in two inbred chicken lines using small RNA sequencing on the Illumina HiSeq2000 platform. The authors compared miRNA expression across the two chicken lines and found that some miRNAs are differentially altered in response to NE and they modulate the expression of their target genes. Collectively, HTS analysis of intestinal miRNAs from NE-afflicted inbred chickens showing different disease phenotypes led to the identification of host immunity genes regulated by miRNA.

Abstract Illumina Summary

Abstract

Avian pathogenic Escherichia coli (APEC) are responsible for heavy economic losses in poultry industry. Here we investigate DNA methylome of spleen and identify functional DNA methylation changes related to host response to APEC among groups of non-challenged chickens (NC), challenged with mild (MD) and severe pathology (SV). DNA methylation was enriched in the gene bodies and repeats. Promoter and CGIs are hypomethylated. Integration analysis revealed 22, 87, and 9 genes exhibiting inversely changed DNA methylation and gene expression in NC vs. MD, NC vs. SV, and MD vs. SV, respectively. IL8, IL2RB, and IL1RAPL1 were included. Gene network analysis suggested that besides inflammatory response, other networks and pathways such as organismal injury and abnormalities, cell signaling and molecular transport, are probably related to host response to APEC infection. Moreover, methylation changes in cell cycle processes might contribute to the lesion phenotype differences between MD and SV.

Illumina Summary

Avian colibacillosis (APEC) is one of the most frequent infectious diseases responsible for heavy economic losses in the poultry industry. In this study the authors investigated the DNA methylome of spleen in response to APEC infection. The authors used the MeDip-seq protocol for library preparation and the Illumina HiSeq2000 for sequencing. The authors found that besides inflammatory response, other networks and pathways such as organismal injury and abnormalities, cell signaling and molecular transport, are probably related to host response to APEC infection.

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice.

Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X

Proc Natl
Acad Sci U S
A 111 3877-82

2014

Abstract Illumina Summary

Abstract

Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ~82% were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs.

Illumina Summary

Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. In this study, the authors show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. The authors used Illumina deep sequencing to identify 535,054 24-nt siRNA clusters of which ~82% were OSDCL3a-dependent and showed significant enrichment of miniature inverted repeat TEs.

Abstract

Abstract

Fruit ripening is a complex, genetically programmed process that occurs in conjunction with the differentiation of chloroplasts into chromoplasts and involves changes to the organoleptic properties of the fruit. In this study, an integrative analysis of the transcriptome and proteome was performed to identify important regulators and pathways involved in fruit ripening in a spontaneous late-ripening mutant ('Fengwan' orange, Citrus sinensis L. Osbeck) and its wild type ('Fengjie 72-1'). At the transcript level, 628 genes showed a 2-fold or more expression difference between the mutant and wild type as detected by an RNA sequencing approach. At the protein level, 130 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. A comparison of the transcriptome and proteome data revealed some aspects of the regulation of metabolism during orange fruit ripening. First, a large number of differential genes were found to belong to the plant hormone pathways and cell-wall-related metabolism. Secondly, we noted a correlation between ripening-associated transcripts and sugar metabolites, which suggests the importance of these metabolic pathways during fruit ripening. Thirdly, a number of genes showed inconsistency between the transcript and protein level, which is indicative of post-transcriptional events. These results reveal multiple ripening-associated events during citrus ripening and provide new insights into the molecular mechanisms underlying citrus ripening regulatory networks.

Illumina Summary

Single-cell genomics and single-cell transcriptomics have emerged as powerful tools to study the biology of single cells at a genome-wide scale. In this breakthrough paper, the authors demonstrate how they extracted both DNA and mRNA from the same cell to perform complete transcriptome and genome analysis. Using a quasilinear amplification strategy and Illumina HiSeq for sequencing, they show that the efficiency of their approach is similar to existing methods for single-cell sequencing of either genomic DNA or mRNA. In addition, they found that genes with high cell-to-cell variability in transcript numbers generally have lower genomic copy numbers, and vice versa.

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice.

Sakai H, Kanamori H, Arai-Kichise Y, Shibata-Hatta M, Ebana K, Oono Y, Kurita K, Fujisawa H, Katagiri S, Mukai Y, Hamada M, Itoh T, Matsumoto T, Katayose Y, Wakasa K, Yano M, Wu J

DNA Res

2014

Abstract Illumina Summary

Abstract

Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.

Illumina Summary

The Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. In this study, the authors used Illumina GAIIx and HiSeq whole-genome sequencing of the aus rice cultivar Kasalath to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.

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