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Morino Y. Dynamic evolutionary history of spiralian-specific TALE homeobox genes in mollusks. Dev Growth Differ 2022; 64:198-209. [PMID: 35441397 DOI: 10.1111/dgd.12779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
Homeobox genes play essential roles in the early development of many animals. Although the repertoire of most homeobox genes, including three amino acid loop extension (TALE)-type homeobox genes, is conserved in animals, spiralian-TALE (SPILE) genes are a notable exception. In this study, SPILE genes were extracted from the genomic data of 22 mollusk species and classified into four clades (-A/C, -B, -D, and -E) to determine which SPILE genes exhibit dynamic repertoire changes. While SPILE-D and -E duplications were rarely observed, SPILE-B duplication was observed in the bivalve lineage and SPILE-A/C duplication was observed in multiple clades. Conversely, most or all SPILE genes were lost in cephalopods and in some gastropod lineages. SPILE gene expression patterns were also analyzed in multiple mollusk species using publicly available RNA-seq data. The majority of SPILE genes examined, particularly those in the A/C- and B-clades, were specifically expressed during early development, suggesting that most SPILE genes exert specific roles in early development. This comprehensive cataloging and characterization revealed a dynamic evolutionary history, including SPILE-A/C and -B gene duplications and the loss of SPILE genes in several lineages. Furthermore, this study provides a useful resource for studying the molecular mechanism of spiralian early development and the evolution of young and lineage-specific transcription factors.
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Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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2
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Genes with spiralian-specific protein motifs are expressed in spiralian ciliary bands. Nat Commun 2020; 11:4171. [PMID: 32820176 PMCID: PMC7441323 DOI: 10.1038/s41467-020-17780-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
Spiralia is a large, ancient and diverse clade of animals, with a conserved early developmental program but diverse larval and adult morphologies. One trait shared by many spiralians is the presence of ciliary bands used for locomotion and feeding. To learn more about spiralian-specific traits we have examined the expression of 20 genes with protein motifs that are strongly conserved within the Spiralia, but not detectable outside of it. Here, we show that two of these are specifically expressed in the main ciliary band of the mollusc Tritia (also known as Ilyanassa). Their expression patterns in representative species from five more spiralian phyla—the annelids, nemerteans, phoronids, brachiopods and rotifers—show that at least one of these, lophotrochin, has a conserved and specific role in particular ciliated structures, most consistently in ciliary bands. These results highlight the potential importance of lineage-specific genes or protein motifs for understanding traits shared across ancient lineages. Spiralians have ciliary bands, used for locomotion and feeding, but defining molecular features of these structures are unknown. Here, the authors report a gene, Lophotrochin, that contains a protein domain only found in spiralians, and specifically expressed in diverse ciliary bands across the group, which provides a molecular signature for these structures.
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Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. Int J Genomics 2017; 2017:8614160. [PMID: 28154822 PMCID: PMC5244023 DOI: 10.1155/2017/8614160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/28/2016] [Indexed: 01/22/2023] Open
Abstract
Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.
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Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster, Pinctada fucata, Based on Transcriptome Analysis. Int J Genomics 2016; 2016:2895303. [PMID: 27843935 PMCID: PMC5097826 DOI: 10.1155/2016/2895303] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/26/2016] [Accepted: 09/20/2016] [Indexed: 11/27/2022] Open
Abstract
P. fucata experiences a series of transformations in appearance, from swimming larvae to sessile juveniles, during which significant changes in gene expression likely occur. Thus, P. fucata could be an ideal model in which to study the molecular mechanisms of larval metamorphosis during development in invertebrates. To study the molecular driving force behind metamorphic development in larvae of P. fucata, transcriptomes of five larval stages (trochophore, D-shape, umbonal, eyespots, and spats) were sequenced using an Illumina HiSeq™ 2000 system and assembled and characterized with the transcripts of six tissues. As a result, a total of 174,126 unique transcripts were assembled and 60,999 were annotated. The number of unigenes varied among the five larval stages. Expression profiles were distinctly different between trochophore, D-shape, umbonal, eyespots, and spats larvae. As a result, 29 expression trends were sorted, of which eight were significant. Among others, 80 development-related, differentially expressed unigenes (DEGs) were identified, of which the majority were homeobox-containing genes. Most DEGs occurred among trochophore, D-shaped, and UES (umbonal, eyespots, and spats) larvae as verified by qPCR. Principal component analysis (PCA) also revealed significant differences in expression among trochophore, D-shaped, and UES larvae with ten transcripts identified but no matching annotations.
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5
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Chou HC, Pruitt MM, Bastin BR, Schneider SQ. A transcriptional blueprint for a spiral-cleaving embryo. BMC Genomics 2016; 17:552. [PMID: 27496340 PMCID: PMC4974748 DOI: 10.1186/s12864-016-2860-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/29/2016] [Indexed: 01/29/2023] Open
Abstract
Background The spiral cleavage mode of early development is utilized in over one-third of all animal phyla and generates embryonic cells of different size, position, and fate through a conserved set of stereotypic and invariant asymmetric cell divisions. Despite the widespread use of spiral cleavage, regulatory and molecular features for any spiral-cleaving embryo are largely uncharted. To address this gap we use RNA-sequencing on the spiralian model Platynereis dumerilii to capture and quantify the first complete genome-wide transcriptional landscape of early spiral cleavage. Results RNA-sequencing datasets from seven stages in early Platynereis development, from the zygote to the protrochophore, are described here including the de novo assembly and annotation of ~17,200 Platynereis genes. Depth and quality of the RNA-sequencing datasets allow the identification of the temporal onset and level of transcription for each annotated gene, even if the expression is restricted to a single cell. Over 4000 transcripts are maternally contributed and cleared by the end of the early spiral cleavage phase. Small early waves of zygotic expression are followed by major waves of thousands of genes, demarcating the maternal to zygotic transition shortly after the completion of spiral cleavages in this annelid species. Conclusions Our comprehensive stage-specific transcriptional analysis of early embryonic stages in Platynereis elucidates the regulatory genome during early spiral embryogenesis and defines the maternal to zygotic transition in Platynereis embryos. This transcriptome assembly provides the first systems-level view of the transcriptional and regulatory landscape for a spiral-cleaving embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2860-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hsien-Chao Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Margaret M Pruitt
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.,Present Address: Department of Pediatrics, University of Chicago, Chicago, IL, USA
| | - Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA, 50011, USA.
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6
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Goulding MQ, Lambert JD. Mollusc models I. The snail Ilyanassa. Curr Opin Genet Dev 2016; 39:168-174. [PMID: 27497839 DOI: 10.1016/j.gde.2016.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/07/2016] [Accepted: 07/07/2016] [Indexed: 11/27/2022]
Abstract
Ilyanassa obsoleta has been a model system for experimental embryology for over a century. Here we highlight new insight into early cell lineage specification in Ilyanassa. As in all molluscs and other spiralians, stereotyped cleavage patterns establish a homunculus of regional founder cells. Ongoing studies are beginning to dissect mechanisms of asymmetric cell division that specify these cells' fates. This is only part of the story: overlaid on intrinsic cell identities is a graded 'organizer' signal, and emerging evidence suggests wider roles for short-range intercellular signaling. Modern methods, combined with the intrinsic experimental advantages of Ilyanassa, offer attractive opportunities for studying basic developmental cell biology as well as its evolution over a wide range of phylogenetic scales.
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Affiliation(s)
- Morgan Q Goulding
- Division of Natural Science, Bethel University, McKenzie, TN 38201, United States.
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY 14627, United States.
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Niu D, Wang F, Xie S, Sun F, Wang Z, Peng M, Li J. Developmental Transcriptome Analysis and Identification of Genes Involved in Larval Metamorphosis of the Razor Clam, Sinonovacula constricta. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:168-175. [PMID: 26921240 DOI: 10.1007/s10126-016-9691-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
The razor clam Sinonovacula constricta is an important commercial species. The deficiency of developmental transcriptomic data is becoming the bottleneck of further researches on the mechanisms underlying settlement and metamorphosis in early development. In this study, de novo transcriptome sequencing was performed for S. constricta at different early developmental stages by using Illumina HiSeq 2000 paired-end (PE) sequencing technology. A total of 112,209,077 PE clean reads were generated. De novo assembly generated 249,795 contigs with an average length of 585 bp. Gene annotation resulted in the identification of 22,870 unigene hits against the NCBI database. Eight unique sequences related to metamorphosis were identified and analyzed using real-time PCR. The razor clam reference transcriptome would provide useful information on early developmental and metamorphosis mechanisms and could be used in the genetic breeding of shellfish.
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Affiliation(s)
- Donghong Niu
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China
| | - Fei Wang
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China
| | - Shumei Xie
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China
| | - Fanyue Sun
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Developmental Biology, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ze Wang
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China
| | - Maoxiao Peng
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China
| | - Jiale Li
- Shanghai Engineering Research Center of Aquaculture and College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, China.
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8
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Barucca M, Canapa A, Biscotti MA. An Overview of Hox Genes in Lophotrochozoa: Evolution and Functionality. J Dev Biol 2016; 4:jdb4010012. [PMID: 29615580 PMCID: PMC5831810 DOI: 10.3390/jdb4010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/02/2016] [Accepted: 03/12/2016] [Indexed: 11/29/2022] Open
Abstract
Hox genes are regulators of animal embryonic development. Changes in the number and sequence of Hox genes as well as in their expression patterns have been related to the evolution of the body plan. Lophotrochozoa is a clade of Protostomia characterized by several phyla which show a wide morphological diversity. Despite that the works summarized in this review emphasize the fragmentary nature of the data available regarding the presence and expression of Hox genes, they also offer interesting insight into the evolution of the Hox cluster and the role played by Hox genes in several phyla. However, the number of genes involved in the cluster of the lophotrochozoan ancestor is still a question of debate. The data presented here suggest that at least nine genes were present while two other genes, Lox4 and Post-2, may either have been present in the ancestor or may have arisen as a result of duplication in the Brachiopoda-Mollusca-Annelida lineage. Spatial and temporal collinearity is a feature of Hox gene expression which was probably present in the ancestor of deuterostomes and protostomes. However, in Lophotrochozoa, it has been detected in only a few species belonging to Annelida and Mollusca.
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Affiliation(s)
- Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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9
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Dhanyalakshmi KH, Naika MBN, Sajeevan RS, Mathew OK, Shafi KM, Sowdhamini R, N. Nataraja K. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. PLoS One 2016; 11:e0151323. [PMID: 26982336 PMCID: PMC4794119 DOI: 10.1371/journal.pone.0151323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 02/27/2016] [Indexed: 01/23/2023] Open
Abstract
The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.
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Affiliation(s)
- K. H. Dhanyalakshmi
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | | | - R. S. Sajeevan
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
| | - Oommen K. Mathew
- National Centre for Biological Sciences, TIFR, GKVK campus, Bengaluru, 560065, India
| | - K. Mohamed Shafi
- National Centre for Biological Sciences, TIFR, GKVK campus, Bengaluru, 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, GKVK campus, Bengaluru, 560065, India
- * E-mail: ; (KNN); (RS)
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India
- * E-mail: ; (KNN); (RS)
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Sherman A, Rubinstein M, Eshed R, Benita M, Ish-Shalom M, Sharabi-Schwager M, Rozen A, Saada D, Cohen Y, Ophir R. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome. BMC PLANT BIOLOGY 2015; 15:277. [PMID: 26573148 PMCID: PMC4647706 DOI: 10.1186/s12870-015-0663-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/04/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. RESULTS We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. CONCLUSIONS Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.
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Affiliation(s)
- Amir Sherman
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mor Rubinstein
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ravit Eshed
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Miri Benita
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mazal Ish-Shalom
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Michal Sharabi-Schwager
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ada Rozen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - David Saada
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Yuval Cohen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ron Ophir
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
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Liu MM, Davey JW, Jackson DJ, Blaxter ML, Davison A. A conserved set of maternal genes? Insights from a molluscan transcriptome. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2015; 58:501-11. [PMID: 25690965 PMCID: PMC4594767 DOI: 10.1387/ijdb.140121ad] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The early animal embryo is entirely reliant on maternal gene products for a 'jump-start' that transforms a transcriptionally inactive embryo into a fully functioning zygote. Despite extensive work on model species, it has not been possible to perform a comprehensive comparison of maternally-provisioned transcripts across the Bilateria because of the absence of a suitable dataset from the Lophotrochozoa. As part of an ongoing effort to identify the maternal gene that determines left-right asymmetry in snails, we have generated transcriptome data from 1 to 2-cell and ~32-cell pond snail (Lymnaea stagnalis) embryos. Here, we compare these data to maternal transcript datasets from other bilaterian metazoan groups, including representatives of the Ecydysozoa and Deuterostomia. We found that between 5 and 10% of all L. stagnalis maternal transcripts (~300-400 genes) are also present in the equivalent arthropod (Drosophila melanogaster), nematode (Caenorhabditis elegans), urochordate (Ciona intestinalis) and chordate (Homo sapiens, Mus musculus, Danio rerio) datasets. While the majority of these conserved maternal transcripts ("COMATs") have housekeeping gene functions, they are a non-random subset of all housekeeping genes, with an overrepresentation of functions associated with nucleotide binding, protein degradation and activities associated with the cell cycle. We conclude that a conserved set of maternal transcripts and their associated functions may be a necessary starting point of early development in the Bilateria. For the wider community interested in discovering conservation of gene expression in early bilaterian development, the list of putative COMATs may be useful resource.
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Affiliation(s)
- M Maureen Liu
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
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12
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Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Annotation of the Protein Coding Regions of the Equine Genome. PLoS One 2015; 10:e0124375. [PMID: 26107351 PMCID: PMC4481266 DOI: 10.1371/journal.pone.0124375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/01/2015] [Indexed: 12/30/2022] Open
Abstract
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.
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Affiliation(s)
- Matthew S. Hestand
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Theodore S. Kalbfleisch
- Biochemistry and Molecular Biology Department, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Stephen J. Coleman
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zheng Zeng
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James N. MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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13
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Biscotti MA, Canapa A, Forconi M, Barucca M. HoxandParaHoxgenes: A review on molluscs. Genesis 2014; 52:935-45. [DOI: 10.1002/dvg.22839] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; Ancona Italy
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14
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Molecular conservation of metazoan gut formation: evidence from expression of endomesoderm genes in Capitella teleta (Annelida). EvoDevo 2014; 5:39. [PMID: 25908956 PMCID: PMC4407770 DOI: 10.1186/2041-9139-5-39] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 09/17/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Metazoan digestive systems develop from derivatives of ectoderm, endoderm and mesoderm, and vary in the relative contribution of each germ layer across taxa and between gut regions. In a small number of well-studied model systems, gene regulatory networks specify endoderm and mesoderm of the gut within a bipotential germ layer precursor, the endomesoderm. Few studies have examined expression of endomesoderm genes outside of those models, and thus, it is unknown whether molecular specification of gut formation is broadly conserved. In this study, we utilize a sequenced genome and comprehensive fate map to correlate the expression patterns of six transcription factors with embryonic germ layers and gut subregions during early development in Capitella teleta. RESULTS The genome of C. teleta contains the five core genes of the sea urchin endomesoderm specification network. Here, we extend a previous study and characterize expression patterns of three network orthologs and three additional genes by in situ hybridization during cleavage and gastrulation stages and during formation of distinct gut subregions. In cleavage stage embryos, Ct-otx, Ct-blimp1, Ct-bra and Ct-nkx2.1a are expressed in all four macromeres, the endoderm precursors. Ct-otx, Ct-blimp1, and Ct-nkx2.1a are also expressed in presumptive endoderm of gastrulae and later during midgut development. Additional gut-specific expression patterns include Ct-otx, Ct-bra, Ct-foxAB and Ct-gsc in oral ectoderm; Ct-otx, Ct-blimp1, Ct-bra and Ct-nkx2.1a in the foregut; and both Ct-bra and Ct-nkx2.1a in the hindgut. CONCLUSIONS Identification of core sea urchin endomesoderm genes in C. teleta indicates they are present in all three bilaterian superclades. Expression of Ct-otx, Ct-blimp1 and Ct-bra, combined with previously published Ct-foxA and Ct-gataB1 patterns, provide the most comprehensive comparison of these five orthologs from a single species within Spiralia. Each ortholog is likely involved in endoderm specification and midgut development, and several may be essential for establishment of the oral ectoderm, foregut and hindgut, including specification of ectodermal and mesodermal contributions. When the five core genes are compared across the Metazoa, their conserved expression patterns suggest that 'gut gene' networks evolved to specify distinct digestive system subregions, regardless of species-specific differences in gut architecture or germ layer contributions within each subregion.
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Ho KKY, Leung PTY, Ip JCH, Qiu JW, Leung KMY. De novo transcriptomic profile in the gonadal tissues of the intertidal whelk Reishia clavigera. MARINE POLLUTION BULLETIN 2014; 85:499-504. [PMID: 24629602 DOI: 10.1016/j.marpolbul.2014.02.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/15/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
The intertidal whelk Reishia clavigera (formerly named as Thais clavigera) is one of the most sensitive species to organotin-associated imposex. However, the limited information on mRNA transcriptome of the species has restricted the molecular investigation on such endocrine disruption. By means of Illumina sequencing, we obtained a global de novo transcriptome from the gonadal tissues of both male and female R. clavigera, with 197,324 assembled transcripts and 151,684 condensed non-redundant transcripts. Blast hit results from the NCBI's non-redundant molluscan database showed that 28,948 transcripts were successfully annotated with significant matches at an e-value of ⩽1e(-6). Among them, 1108 transcripts were assigned a well-defined gene ontology term. As the first transcriptomic study on the gonadal tissues of R. clavigera, this study has enhanced the information of mRNA transcriptome on this species and will thus facilitate mechanistic studies of chemical contaminants (e.g., organotins) on this common biomonitor species.
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Affiliation(s)
- Kevin K Y Ho
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Priscilla T Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jack C H Ip
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - J W Qiu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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Eierman LE, Hare MP. Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica. BMC Genomics 2014; 15:503. [PMID: 24950855 PMCID: PMC4101419 DOI: 10.1186/1471-2164-15-503] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/03/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The eastern oyster, Crassostrea virginica, is a euryhaline species that can thrive across a wide range of salinities (5-35). As with all estuarine species, individual oysters must be able to regulate their osmotic balance in response to constant temporal variation in salinity. At the population level, recurrent viability selection may be an additional mechanism shaping adaptive osmoregulatory phenotypes at the margins of oyster salinity tolerance. To identify candidate genes for osmoregulation, we sequenced, assembled, and annotated the transcriptome of wild juvenile eastern oysters from 'high' and 'low' salinity regimes. Annotations and candidates were mostly based on the Pacific oyster (Crassostrea gigas) genome sequence so osmoregulatory relevance in C. virginica was explored by testing functional enrichment of genes showing spatially discrete patterns of expression and by quantifying coding sequence divergence. RESULTS The assembly of sequence reads and permissive clustering of potentially oversplit alleles resulted in 98,729 reftigs (contigs and singletons). Of these, 50,736 were annotated with 9,307 belonging to a set of candidate osmoregulatory genes identified from the C. gigas genome. A total of 218,777 SNPs (0.0185 SNPs/bp) were identified in annotated reftigs of C. virginica. Amino acid divergence between translations of C. virginica annotated reftigs and C. gigas coding sequence averaged 23.2 % with an average dN/dS ratio of 0.074, suggesting purifying selection on protein sequences. The high and low salinity source oysters each expressed a subset of genes unique to that group, and the functions for these annotated genes were consistent with known molecular mechanisms for osmotic regulation in molluscs. CONCLUSIONS Most of the osmoregulatory gene candidates experimentally identified in C. gigas are present in this C. virginica transcriptome. In general these congeners show coding sequence divergence too high to make the C. gigas genome a useful reference for C. virginica bioinformatics. However, strong purifying selection is characteristic of the osmoregulatory candidates so functional annotations are likely to correspond. An initial examination of C. virginica presence/absence expression patterns across the salinity gradient in a single estuary suggests that many of these candidates have expression patterns that co-vary with salinity, consistent with osmoregulatory function in C. virginica.
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Affiliation(s)
- Laura E Eierman
- Department of Natural Resources, Cornell University, 213 Bradfield Hall, Ithaca, NY 14853 USA
| | - Matthew P Hare
- Department of Natural Resources, Cornell University, 213 Bradfield Hall, Ithaca, NY 14853 USA
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Matsumoto T, Masaoka T, Fujiwara A, Nakamura Y, Satoh N, Awaji M. Reproduction-related genes in the pearl oyster genome. Zoolog Sci 2013; 30:826-50. [PMID: 24125647 DOI: 10.2108/zsj.30.826] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molluscan reproduction has been a target of biological research because of the various reproductive strategies that have evolved in this phylum. It has also been studied for the development of fisheries technologies, particularly aquaculture. Although fundamental processes of reproduction in other phyla, such as vertebrates and arthropods, have been well studied, information on the molecular mechanisms of molluscan reproduction remains limited. The recently released draft genome of the pearl oyster Pinctada fucata provides a novel and powerful platform for obtaining structural information on the genes and proteins involved in bivalve reproduction. In the present study, we analyzed the pearl oyster draft genome to screen reproduction-related genes. Analysis was mainly conducted for genes reported from other molluscs for encoding orthologs of reproduction-related proteins in other phyla. The gene search in the P. fucata gene models (version 1.1) and genome assembly (version 1.0) were performed using Genome Browser and BLAST software. The obtained gene models were then BLASTP searched against a public database to confirm the best-hit sequences. As a result, more than 40 gene models were identified with high accuracy to encode reproduction-related genes reported for P. fucata and other molluscs. These include vasa, nanos, doublesex- and mab-3-related transcription factor, 5-hydroxytryptamine (5-HT) receptors, vitellogenin, estrogen receptor, and others. The set of reproduction-related genes of P. fucata identified in the present study constitute a new tool for research on bivalve reproduction at the molecular level.
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Affiliation(s)
- Toshie Matsumoto
- 1 Aquaculture Technology Division, National Research Institute of Aquaculture, Fisheries Research Agency, Minami-lse, Watarai, Mie 516-0193, Japan
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Agunbiade TA, Sun W, Coates BS, Djouaka R, Tamò M, Ba MN, Binso-Dabire C, Baoua I, Olds BP, Pittendrigh BR. Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PLoS One 2013; 8:e79929. [PMID: 24278221 PMCID: PMC3838393 DOI: 10.1371/journal.pone.0079929] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, Anoplocnemis curvipes Fabricius (Hemiptera: Coreidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, Aphis craccivora Koch (Hemiptera: Aphididae) and flower thrips, Megalurothrips sjostedti Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. The reads were de novo assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, Buchnera aphidicola, were identified among A. craccivora transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa.
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Affiliation(s)
- Tolulope A. Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brad S. Coates
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | | | - Manuele Tamò
- International Institute of Tropical Agriculture, Cotonou, Benin
| | - Malick N. Ba
- Institut de l’Environnement et de Recherches Agricoles, Ouagadougou, Burkina Faso
| | | | - Ibrahim Baoua
- Institut National de la Recherche Agronomique du Niger, Maradi, Niger
| | - Brett P. Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Raymond JA, Morgan-Kiss R. Separate origins of ice-binding proteins in antarctic chlamydomonas species. PLoS One 2013; 8:e59186. [PMID: 23536869 PMCID: PMC3594216 DOI: 10.1371/journal.pone.0059186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/12/2013] [Indexed: 11/22/2022] Open
Abstract
The green alga Chlamydomonas raudensis is an important primary producer in a number of ice-covered lakes and ponds in Antarctica. A C. raudensis isolate (UWO241) from Lake Bonney in the McMurdo Dry Valleys, like many other Antarctic algae, was found to secrete ice-binding proteins (IBPs), which appear to be essential for survival in icy environments. The IBPs of several Antarctic algae (diatoms, a prymesiophyte, and a prasinophyte) are similar to each other (here designated as type I IBPs) and have been proposed to have bacterial origins. Other IBPs (type II IBPs) that bear no resemblance to type I IBPs, have been found in the Antarctic Chlamydomonas sp. CCMP681, a putative snow alga, raising the possibility that chlamydomonad IBPs developed separately from the IBPs of other algae. To test this idea, we obtained the IBP sequences of C. raudensis UWO241 by sequencing the transcriptome. A large number of transcripts revealed no sequences resembling type II IBPs. Instead, many isoforms resembling type I IBPs were found, and these most closely matched a hypothetical protein from the bacterium Stigmatella aurantiaca. The sequences were confirmed to encode IBPs by the activity of a recombinant protein and by the matching of predicted and observed isoelectric points and molecular weights. Furthermore, a mesophilic sister species, C. raudensis SAG49.72, showed no ice-binding activity or PCR products from UWO241 IBP primers. These results confirm that algal IBPs are required for survival in icy habitats and demonstrate that they have diverse origins that are unrelated to the taxonomic positions of the algae. Last, we show that the C. raudensis UWO241 IBPs can change the structure of ice in a way that could increase the survivability of cells trapped in the ice.
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Affiliation(s)
- James A Raymond
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America.
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20
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Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 2013; 8:e55731. [PMID: 23383346 PMCID: PMC3562227 DOI: 10.1371/journal.pone.0055731] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 12/29/2012] [Indexed: 01/10/2023] Open
Abstract
Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.
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Affiliation(s)
- Jacqueline M. Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, United States of America
| | - Dayakar V. Badri
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, United States of America
| | - Matthew G. Bakker
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, United States of America
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Daniel K. Manter
- United States Department of Agriculture - Agricultural Research Service, Soil-Plant-Nutrient Research Unit, Fort Collins, Colorado, United States of America
| | - Jorge M. Vivanco
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, United States of America
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Huang ZX, Chen ZS, Ke CH, Zhao J, You WW, Zhang J, Dong WT, Chen J. Pyrosequencing of Haliotis diversicolor transcriptomes: insights into early developmental molluscan gene expression. PLoS One 2012; 7:e51279. [PMID: 23236463 PMCID: PMC3517415 DOI: 10.1371/journal.pone.0051279] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/31/2012] [Indexed: 12/02/2022] Open
Abstract
Background The abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking. Methodology/Principal Findings In this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the ‘lock system’ in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae. Conclusion This study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.
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Affiliation(s)
- Zi-Xia Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Zhi-Sen Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Cai-Huan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jing Zhao
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Wei You
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jie Zhang
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Ting Dong
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jun Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
- * E-mail:
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Mitchell RF, Hughes DT, Luetje CW, Millar JG, Soriano-Agatón F, Hanks LM, Robertson HM. Sequencing and characterizing odorant receptors of the cerambycid beetle Megacyllene caryae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:499-505. [PMID: 22504490 PMCID: PMC3361640 DOI: 10.1016/j.ibmb.2012.03.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/19/2012] [Accepted: 03/23/2012] [Indexed: 05/05/2023]
Abstract
Odorant receptors (Ors) are a unique family of ligand-gated ion channels and the primary mechanism by which insects detect volatile chemicals. Here, we describe 57 putative Ors sequenced from an antennal transcriptome of the cerambycid beetle Megacyllene caryae (Gahan). The male beetles produce a pheromone blend of nine compovnents, and we functionally characterized Ors tuned to three of these chemicals: receptor McOr3 is sensitive to (S)-2-methyl-1-butanol; McOr20 is sensitive to (2S,3R)-2,3-hexanediol; and McOr5 is sensitive to 2-phenylethanol. McOr3 and McOr20 are also sensitive to structurally-related chemicals that are pheromones of other cerambycid beetles, suggesting that orthologous receptors may be present across many cerambycid species. These Ors are the first to be functionally characterized from any species of beetle and lay the groundwork for understanding the evolution of pheromones within the Cerambycidae.
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Affiliation(s)
- Robert F. Mitchell
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - David T. Hughes
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, 33136
| | - Charles W. Luetje
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, 33136
| | - Jocelyn G. Millar
- Department of Entomology, University of California, Riverside, CA 92521
| | | | - Lawrence M. Hanks
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- To whom correspondence should be addressed. , phone: 217-333-0489, fax: 217-244-3499
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Nyberg KG, Conte MA, Kostyun JL, Forde A, Bely AE. Transcriptome characterization via 454 pyrosequencing of the annelid Pristina leidyi, an emerging model for studying the evolution of regeneration. BMC Genomics 2012; 13:287. [PMID: 22747785 PMCID: PMC3464666 DOI: 10.1186/1471-2164-13-287] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 06/29/2012] [Indexed: 11/23/2022] Open
Abstract
Background The naid annelids contain a number of species that vary in their ability to regenerate lost body parts, making them excellent candidates for evolution of regeneration studies. However, scant sequence data exists to facilitate such studies. We constructed a cDNA library from the naid Pristina leidyi, a species that is highly regenerative and also reproduces asexually by fission, using material from a range of regeneration and fission stages for our library. We then sequenced the transcriptome of P. leidyi using 454 technology. Results 454 sequencing produced 1,550,174 reads with an average read length of 376 nucleotides. Assembly of 454 sequence reads resulted in 64,522 isogroups and 46,679 singletons for a total of 111,201 unigenes in this transcriptome. We estimate that over 95% of the transcripts in our library are present in our transcriptome. 17.7% of isogroups had significant BLAST hits to the UniProt database and these include putative homologs of a number of genes relevant to regeneration research. Although many sequences are incomplete, the mean sequence length of transcripts (isotigs) is 707 nucleotides. Thus, many sequences are large enough to be immediately useful for downstream applications such as gene expression analyses. Using in situ hybridization, we show that two Wnt/β-catenin pathway genes (homologs of frizzled and β-catenin) present in our transcriptome are expressed in the regeneration blastema of P. leidyi, demonstrating the usefulness of this resource for regeneration research. Conclusions 454 sequencing is a rapid and efficient approach for identifying large numbers of genes in an organism that lacks a sequenced genome. This transcriptome dataset will be a valuable resource for molecular analyses of regeneration in P. leidyi and will serve as a starting point for comparisons to non-regenerating naids. It also contributes significantly to the still limited genomic resources available for annelids and lophotrochozoans more generally.
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Affiliation(s)
- Kevin G Nyberg
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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Olds BP, Coates BS, Steele LD, Sun W, Agunbiade TA, Yoon KS, Strycharz JP, Lee SH, Paige KN, Clark JM, Pittendrigh BR. Comparison of the transcriptional profiles of head and body lice. INSECT MOLECULAR BIOLOGY 2012; 21:257-268. [PMID: 22404397 DOI: 10.1111/j.1365-2583.2012.01132.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Head and body lice are both blood-feeding parasites of humans although only the body louse is a potent disease vector. In spite of numerous morphological and life history differences, head and body lice have recently been hypothesized to be ecotypes of the same species. We took a comparative genomics approach to measure nucleotide diversity by comparing expressed sequence tag data sets from head and body lice. A total of 10 771 body louse and 10 770 head louse transcripts were predicted from a combined assembly of Roche 454 and Illumina sequenced cDNAs from whole body tissues collected at all life stages and during pesticide exposure and bacterial infection treatments. Illumina reads mapped to the 10 775 draft body louse gene models from the whole genome assembly predicted nine presence/absence differences, but PCR confirmation resulted in a single gene difference. Read per million base pair estimates indicated that 14 genes showed significant differential expression between head and body lice under our treatment conditions. One novel microRNA was predicted in both lice species and 99% of the 544 transcripts from Candidatus riesia indicate that they share the same endosymbiont. Overall, few differences exist, which supports the hypothesis that these two organisms are ecotypes of the same species.
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Affiliation(s)
- Brett P Olds
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Canbäck B, André C, Galindo J, Johannesson K, Johansson T, Panova M, Tunlid A, Butlin R. The Littorina sequence database (LSD)--an online resource for genomic data. Mol Ecol Resour 2011; 12:142-8. [PMID: 21707958 DOI: 10.1111/j.1755-0998.2011.03042.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.
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Affiliation(s)
- Björn Canbäck
- Microbial Ecology, Department of Biology, Lund University, SE-223 62 Lund, Sweden
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Chan XY, Lambert JD. Patterning a spiralian embryo: A segregated RNA for a Tis11 ortholog is required in the 3a and 3b cells of the Ilyanassa embryo. Dev Biol 2011; 349:102-12. [DOI: 10.1016/j.ydbio.2010.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 09/29/2010] [Accepted: 10/01/2010] [Indexed: 01/10/2023]
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