Special Issue "Insights from Plant Genomes"

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A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 August 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Tamas Dalmay
School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
Website: http://www.uea.ac.uk/biological-sciences/People/Academic/Tamas+Dalmay#research
E-Mail: t.dalmay@uea.ac.uk

Special Issue Information

Dear Colleagues,

Recent developments in sequencing technology revolutionized molecular biology and had a big impact on plant science. Many genome sequencing projects have been completed generating an unprecedented amount of information. This information can shed light on how species evolved but also helps studying all aspects of plant life at a molecular level. As more and more crop species' genome is sequenced, translation of knowledge from model systems to crops become quicker and easier. This special issue will cover original research papers and reviews on the broad topic of plant genomes.

Professor Tamas Dalmay
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Published Papers (10 papers)

Biology 2014, 3(2), 295-319; doi:10.3390/biology3020295 (doi registration under processing)
Received: 30 October 2013; in revised form: 16 March 2014 / Accepted: 25 March 2014 / Published: 16 April 2014
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Biology 2014, 3(1), 39-55; doi:10.3390/biology3010039
Received: 4 November 2013; in revised form: 3 January 2014 / Accepted: 3 January 2014 / Published: 21 January 2014
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Biology 2013, 2(4), 1465-1487; doi:10.3390/biology2041465
Received: 25 September 2013; in revised form: 19 November 2013 / Accepted: 20 November 2013 / Published: 9 December 2013
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Biology 2013, 2(4), 1378-1410; doi:10.3390/biology2041378
Received: 30 October 2013; in revised form: 15 November 2013 / Accepted: 18 November 2013 / Published: 28 November 2013
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Biology 2013, 2(4), 1357-1377; doi:10.3390/biology2041357
Received: 16 August 2013; in revised form: 29 October 2013 / Accepted: 8 November 2013 / Published: 25 November 2013
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Biology 2013, 2(4), 1338-1356; doi:10.3390/biology2041338
Received: 12 September 2013; in revised form: 8 November 2013 / Accepted: 12 November 2013 / Published: 21 November 2013
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Biology 2013, 2(4), 1311-1337; doi:10.3390/biology2041311
Received: 20 September 2013; in revised form: 6 November 2013 / Accepted: 12 November 2013 / Published: 21 November 2013
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Biology 2013, 2(4), 1224-1241; doi:10.3390/biology2041224
Received: 18 September 2013; in revised form: 3 October 2013 / Accepted: 8 October 2013 / Published: 18 October 2013
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Biology 2013, 2(4), 1210-1223; doi:10.3390/biology2041210
Received: 27 August 2013; in revised form: 24 September 2013 / Accepted: 25 September 2013 / Published: 30 September 2013
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Biology 2013, 2(3), 1150-1164; doi:10.3390/biology2031150
Received: 6 August 2013; in revised form: 2 September 2013 / Accepted: 5 September 2013 / Published: 12 September 2013
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Title: Analysis of T-DNA/host-plant DNA Junction Sequences in Single-copy Transgenic Barley Lines
Authors: Joanne G Bartlett, Mark A Smedley, Wendy A Harwood*.
Affiliations: Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK; E-Mail: wendy.harwood@jic.ac.uk
Abstract: Sequencing across the junction between an integrated transfer DNA (T-DNA) and a host plant genome provides two important pieces of information. The junctions themselves provide information regarding the proportion of T-DNA which has integrated into the host plant genome, whilst the transgene flanking sequences can be used to study the local genetic environment of the integrated transgene. In addition, this information is important in the safety assessment of GM crops and essential for GM traceability. In this study, a detailed analysis was carried out on the right-border T-DNA junction sequences of single-copy independent transgenic barley lines. T-DNA truncations at the right-border were found to be relatively common and affected 33.3% of the lines. In addition, 14.3% of lines had rearranged construct sequence after the right border break-point. An in depth analysis of the host-plant flanking sequences revealed that a significant proportion of the T-DNAs integrated into or close to known repetitive elements. However, this integration into repetitive DNA did not have a negative effect on transgene expression.

Type of Paper: Article
Title: Possible Involvement of Alternate RNA Splice Variants in Regulating Soybean Seed Development and Metabolism
Authors: Delasa Aghamirzaie 1, Yihui Fang 2, Farzaneh Tabataba 1, Curtis Klumas 2, Lenwood Heath 3, Ruth Grene 2 and Eva Collakova 2,*
Affiliations: 1. Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA
2. Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA; E-Mail: collakov@vt.edu
3. Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
Abstract: Seeds provide means of sexual propagation in plants and represent an important source of food (oils, proteins, and carbohydrates) for humans and animals. Oilseeds of agriculturally important crops including soybean (Glycine max) also provide triacylglycerols that are used in the industrial production of biofuel and oil-based chemicals. These molecules, also referred to as seed storage compounds, are synthesized in developing seeds and provide resources and energy during seed germination before newly established seedlings are capable of photosynthesis. The accumulation of storage compounds in developing seeds is highly regulated at multiple tiers, including transcriptional and post-transcriptional levels. RNA sequencing was used to provide comprehensive information about transcriptomes and their changes as well as the structures of genes based on splicing information in developing soybean embryos during seed filling. Transcriptomic analyses aided in the identification of over 3,400 novel genes that were not predicted to be present in the recently sequenced soybean genome. Further computational analyses lead to the identification of different splice variants and the corresponding changes in their levels on a global scale during embryo development. These different splice variants may play an important role in regulating developmental and metabolic processes occurring in developing oilseed embryos.

Type of Paper: Review
Title: Revealing the Complexity of Alternative Splicing in Arabidopsis by Deep Transcriptome Survey
Authors: Yamile Marquez, Maria Kalyna and Andrea Barta
Affiliations: Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria; E-Mails: yamile.marquez@univie.ac.at (Y.M.); andrea.barta@meduniwien.ac.at (A.B.) ; mariya.kalyna@univie.ac.at (M.K.)
Abstract: Alternative Splicing (AS) is an essential mechanism to increase the complexity of the transcriptome and consequently of the proteome. Recently it has become apparent that in plants alternative splicing is key for plant development and for responses to environmental cues. This involves flowering time control as well as immediate responses to biotic and abiotic stresses. Moreover, this mechanism seems to be pervasive in the adaptation to daily environmental changes (day/night, temperature) through an inner time keeping mechanism the circadian clock. This review will cover newest developments in genomic approaches to alternative splicing research in plants and discuss the mechanisms which are prevalent as well as their regulation with plant splicing factors, with a focus on SR proteins. In addition, the influence of AS on the transcriptome in particular on non-sense mediated decay will be discussed. Examples for alternative splicing regulation of plant development and stress regulation will bed presented.

Type of Paper: Review
Title: DNA Damage Response in Plants: Conserved and Variable Response Compared to Animals
Authors: Kaoru Okamoto Yoshiyama 1, Kengo Sakaguchi 2, and Seisuke Kimura 1
Affiliations: 1 Department of Bioresource and Environmental Sciences, Kyoto Sangyo University; E-Mails: kaoru.o@cc.kyoto-su.ac.jp (K. O. Y.), seisuke@cc.kyoto-su.ac.jp (S. K.)
2 Research Institute for Science and Technology, Tokyo University of Science; E-Mail: kengo@rs.noda.tus.ac.jp
Abstract: The genome of an organism is under constant attack from endogenous and exogenous DNA damaging factors such as reactive radicals, radiation, and genotoxins. Therefore, DNA damage response systems to sense DNA damage, arrest cell cycle, repair DNA lesions, and/or induce programmed cell death is crucial for maintenance of genomic integrity and survival of the organism. Genome sequences revealed that although plants possess many of the DNA damage response factors that are present in the animal systems, they are missing some of the important regulators, such as p53 tumor suppressor. These observations suggest differences in the DNA damage response mechanisms between plants and animals. In this review the DNA damage responses in plants and animals are compared and contrasted. In addition, the function of SOG1, a plant-specific transcription factor that governs the robust response to DNA damage, will be discussed.

Type of Paper: Review
Title: Elucidation of nuclear and organellar genomes of Gossypium hirsutum: Furthering studies of species evolution and applications for crop improvement
Authors: Jocelyn A Moore and Caryl A Chlan*
Affiliations: Biology Department, The University of Louisiana at Lafayette, Lafayette, LA, USA; E-Mail:cchlan@louisiana.edu
Abstract: Plant genomes are larger and more complex than other eukaryotic organisms due to small and large duplication events, recombination and subsequent reorganization of the genetic material. Commercially important cotton (Gossypium hirsutum) is the result of a polyploidization event between Old and New World cottons that occurred over one million years ago. Allotetraploid cotton has properties that are dramatically different from its progenitors - most notably the presence of long, spinnable fibers. Recently, the complete genome of a New World cotton ancestral species, Gossypium raimondii was completed and a draft sequence of the Old World ancestral strain has been developed. This sequence information will enable us to gain insights into the evolution of the cotton genome that may be used to understand the evolution of other plant species. The chloroplast genomes of multiple cotton species and races have been determined. This information has also been used to gain insight into the evolutionary history of cotton. Analysis of the database of nuclear and organellar sequences will facilitate the identification of potential genes of interest and subsequent development of strategies for improving cotton.

Last update: 10 October 2013

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