Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers.

Abstract:

:Although conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization of conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved towards reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. On the basis of cpDNA organization, our analyses revealed that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the 'gnepines' clade. In addition, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favours the removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data help understand the complexity and evolution of cupressophyte cpDNAs.

journal_name

Plant Biotechnol J

authors

Wu CS,Chaw SM

doi

10.1111/pbi.12141

subject

Has Abstract

pub_date

2014-04-01 00:00:00

pages

344-53

issue

3

eissn

1467-7644

issn

1467-7652

journal_volume

12

pub_type

杂志文章
  • Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.).

    abstract::Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, lar...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12009

    authors: Allen AM,Barker GL,Wilkinson P,Burridge A,Winfield M,Coghill J,Uauy C,Griffiths S,Jack P,Berry S,Werner P,Melichar JP,McDougall J,Gwilliam R,Robinson P,Edwards KJ

    更新日期:2013-04-01 00:00:00

  • Enhancing the expression of starch synthase class IV results in increased levels of both transitory and long-term storage starch.

    abstract::Starch is an important renewable raw material with an increasing number of applications. Several attempts have been made to obtain plants that produce modified versions of starch or higher starch yield. Most of the approaches designed to increase the levels of starch have focused on the increment of the amount of ADP-...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2011.00626.x

    authors: Gámez-Arjona FM,Li J,Raynaud S,Baroja-Fernández E,Muñoz FJ,Ovecka M,Ragel P,Bahaji A,Pozueta-Romero J,Mérida Á

    更新日期:2011-12-01 00:00:00

  • Transient expression assays in grapevine: a step towards genetic improvement.

    abstract::In the past few years, the usefulness of transient expression assays has continuously increased for the characterization of unknown gene function and metabolic pathways. In grapevine (Vitis vinifera L.), one of the most economically important fruit crops in the world, recent systematic sequencing projects produced man...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12294

    authors: Jelly NS,Valat L,Walter B,Maillot P

    更新日期:2014-12-01 00:00:00

  • Stacking three late blight resistance genes from wild species directly into African highland potato varieties confers complete field resistance to local blight races.

    abstract::Considered responsible for one million deaths in Ireland and widespread famine in the European continent during the 1840s, late blight, caused by Phytophthora infestans, remains the most devastating disease of potato (Solanum tuberosum L.) with about 15%-30% annual yield loss in sub-Saharan Africa, affecting mainly sm...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13042

    authors: Ghislain M,Byarugaba AA,Magembe E,Njoroge A,Rivera C,Román ML,Tovar JC,Gamboa S,Forbes GA,Kreuze JF,Barekye A,Kiggundu A

    更新日期:2019-06-01 00:00:00

  • OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development.

    abstract::The rice root system is important for growth. The crosstalk between auxin and cytokinin mediates root initiation and elongation. However, it remains unclear how the transcriptional network upstream of the auxin and cytokinin signalling pathways determines root development. Here, we observed that the knockdown of OsNAC...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13209

    authors: Mao C,He J,Liu L,Deng Q,Yao X,Liu C,Qiao Y,Li P,Ming F

    更新日期:2020-02-01 00:00:00

  • Recombinant aryl hydrocarbon receptors for bioassay of aryl hydrocarbon receptor ligands in transgenic tobacco plants.

    abstract::Dioxin residues widely contaminate soil and agricultural products at low concentrations and may accumulate in organisms at the top of food chains owing to their physicochemical properties. In this study, we have developed novel, dioxin-inducible, reporter gene expression systems regulated by recombinant aryl hydrocarb...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2008.00378.x

    authors: Kodama S,Okada K,Akimoto K,Inui H,Ohkawa H

    更新日期:2009-02-01 00:00:00

  • The origins and progress of genomics research on Tef (Eragrostis tef).

    abstract::Tef, Eragrostis tef (Zucc.) Trotter, is the most important cereal in Ethiopia. Tef is cultivated by more than five million small-scale farmers annually and constitutes the staple food for more than half of the population of 80 million. The crop is preferred by both farmers and consumers due to its beneficial traits as...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12199

    authors: Girma D,Assefa K,Chanyalew S,Cannarozzi G,Kuhlemeier C,Tadele Z

    更新日期:2014-06-01 00:00:00

  • Divergent improvement of two cultivated allotetraploid cotton species.

    abstract::Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid Gossypium spe...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13547

    authors: Fang L,Zhao T,Hu Y,Si Z,Zhu X,Han Z,Liu G,Wang S,Ju L,Guo M,Mei H,Wang L,Qi B,Wang H,Guan X,Zhang T

    更新日期:2021-01-14 00:00:00

  • Commercialization of new biotechnology: a systematic review of 16 commercial case studies in a novel manufacturing sector.

    abstract::The 1980s and 1990s saw a major expansion of biotechnology into new areas of science including genomics and recombinant technologies. This was coupled to the widespread emergence of academics into the commercial sector as they were encouraged to spin out companies or commercialize their intellectual property. There we...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12426

    authors: Paul MJ,Thangaraj H,Ma JK

    更新日期:2015-10-01 00:00:00

  • An AGAMOUS intron-driven cytotoxin leads to flowerless tobacco and produces no detrimental effects on vegetative growth of either tobacco or poplar.

    abstract::Flowerless trait is highly desirable for poplar because it can prevent pollen- and seed-mediated transgene flow. We have isolated the second intron of PTAG2, an AGAMOUS (AG) orthologue from Populus trichocarpa. By fusing this intron sequence to a minimal 35S promoter sequence, we created two artificial promoters, fPTA...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12581

    authors: Li W,Hu W,Fang C,Chen L,Zhuang W,Katin-Grazzini L,McAvoy RJ,Guillard K,Li Y

    更新日期:2016-12-01 00:00:00

  • Characterization of scientific studies usually cited as evidence of adverse effects of GM food/feed.

    abstract::GM crops are the most studied crops in history. Approximately 5% of the safety studies on them show adverse effects that are a cause for concern and tend to be featured in media reports. Although these reports are based on just a handful of GM events, they are used to cast doubt on all GM crops. Furthermore, they tend...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12798

    authors: Sánchez MA,Parrott WA

    更新日期:2017-10-01 00:00:00

  • Haplotyping and mapping a large cluster of downy mildew resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms.

    abstract::Downy mildew (Plasmopara halstedii (Farl.) Berlese et de Toni) is a serious foliar pathogen of cultivated sunflower (Helianthus annuus L.). Genetic resistance is conditioned by several linked downy mildew resistance gene specificities in the HaRGC1 cluster of TIR-NBS-LRR resistance gene candidates (RGCs) on linkage gr...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1046/j.1467-7652.2003.00016.x

    authors: Slabaugh MB,Yu JK,Tang S,Heesacker A,Hu X,Lu G,Bidney D,Han F,Knapp SJ

    更新日期:2003-05-01 00:00:00

  • Whole-genome re-sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad-based resistance to soybean cyst nematode.

    abstract::Soybean cyst nematode (SCN) is the most devastating plant-parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1-b locus, while 'Peki...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13086

    authors: Patil GB,Lakhssassi N,Wan J,Song L,Zhou Z,Klepadlo M,Vuong TD,Stec AO,Kahil SS,Colantonio V,Valliyodan B,Rice JH,Piya S,Hewezi T,Stupar RM,Meksem K,Nguyen HT

    更新日期:2019-08-01 00:00:00

  • Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

    abstract::The plant pathogen, Pseudomonas syringae (Ps), together with related Ps species, infects and attacks a wide range of agronomically important crops, including tomato, kiwifruit, pepper, olive and soybean, causing economic losses. Currently, chemicals and introduced resistance genes are used to protect plants against th...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13294

    authors: Rooney WM,Grinter RW,Correia A,Parkhill J,Walker DC,Milner JJ

    更新日期:2020-05-01 00:00:00

  • Overexpression of Hevea brasiliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation.

    abstract::Ethylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF-IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting str...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12774

    authors: Lestari R,Rio M,Martin F,Leclercq J,Woraathasin N,Roques S,Dessailly F,Clément-Vidal A,Sanier C,Fabre D,Melliti S,Suharsono S,Montoro P

    更新日期:2018-01-01 00:00:00

  • Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.

    abstract::Sumoylation is a posttranslational regulatory process in higher eukaryotes modifying substrate proteins through conjugation of small ubiquitin-related modifiers (SUMOs). Sumoylation modulates protein stability, subcellular localization and activity; thus, it regulates most cellular functions including response to envi...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12030

    authors: Li Z,Hu Q,Zhou M,Vandenbrink J,Li D,Menchyk N,Reighard S,Norris A,Liu H,Sun D,Luo H

    更新日期:2013-05-01 00:00:00

  • Fitness of Bt-resistant cabbage loopers on Bt cotton plants.

    abstract::Development of resistance to the insecticidal toxins from Bacillus thuringiensis (Bt) in insects is the major threat to the continued success of transgenic Bt crops in agriculture. The fitness of Bt-resistant insects on Bt and non-Bt plants is a key parameter that determines the development of Bt resistance in insect ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12718

    authors: Tetreau G,Wang R,Wang P

    更新日期:2017-10-01 00:00:00

  • A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops.

    abstract::Over 3.5 million expressed sequence tags from the major cereal taxa were used to electronically mine over 176,000 putative single nucleotide polymorphisms (SNPs). The density, distribution and degree of linkage between these SNPs were compared among the different taxa. The frequency of sequence polymorphism was lowest...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2009.00412.x

    authors: Barker GL,Edwards KJ

    更新日期:2009-05-01 00:00:00

  • A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines.

    abstract::Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pest affecting soybean production worldwide. SCN resistance requires both the GmSHMT08 and the GmSNAP18 in 'Peking'-type resistance. Here, we describe the molecular interaction between GmSHMT08 and GmSNAP18, which is potentiated by a pathogenesis...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13343

    authors: Lakhssassi N,Piya S,Bekal S,Liu S,Zhou Z,Bergounioux C,Miao L,Meksem J,Lakhssassi A,Jones K,Kassem MA,Benhamed M,Bendahmane A,Lambert K,Boualem A,Hewezi T,Meksem K

    更新日期:2020-08-01 00:00:00

  • RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes.

    abstract::Suppression of the microsomal ω6 oleate desaturase during the seed development of soybean (Glycine max) with the 420-bp soybean FAD2-1A intron as RNAi trigger shifts the conventional fatty acid composition of soybean oil from 20% oleic and 60% polyunsaturates to one containing greater than 80% oleic acid and less than...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00573.x

    authors: Wagner N,Mroczka A,Roberts PD,Schreckengost W,Voelker T

    更新日期:2011-09-01 00:00:00

  • De novo assembly of a wild pear (Pyrus betuleafolia) genome.

    abstract::China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines Pa...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13226

    authors: Dong X,Wang Z,Tian L,Zhang Y,Qi D,Huo H,Xu J,Li Z,Liao R,Shi M,Wahocho SA,Liu C,Zhang S,Tian Z,Cao Y

    更新日期:2020-02-01 00:00:00

  • Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance.

    abstract::Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with co...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12133

    authors: Jain M,Moharana KC,Shankar R,Kumari R,Garg R

    更新日期:2014-02-01 00:00:00

  • Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides.

    abstract::Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and u...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12473

    authors: Rivera-Torres N,Kmiec EB

    更新日期:2016-02-01 00:00:00

  • Stable expression of silencing-suppressor protein enhances the performance and longevity of an engineered metabolic pathway.

    abstract::Transgenic engineering of plants is important in both basic and applied research. However, the expression of a transgene can dwindle over time as the plant's small (s)RNA-guided silencing pathways shut it down. The silencing pathways have evolved as antiviral defence mechanisms, and viruses have co-evolved viral silen...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12506

    authors: Naim F,Shrestha P,Singh SP,Waterhouse PM,Wood CC

    更新日期:2016-06-01 00:00:00

  • Mutations in MIR396e and MIR396f increase grain size and modulate shoot architecture in rice.

    abstract::Grain size and plant architecture are critical factors determining crop productivity. Here, we performed gene editing of the MIR396 gene family in rice and found that MIR396e and MIR396f are two important regulators of grain size and plant architecture. mir396ef mutations can increase grain yield by increasing grain s...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13214

    authors: Miao C,Wang D,He R,Liu S,Zhu JK

    更新日期:2020-02-01 00:00:00

  • FLP recombinase-mediated site-specific recombination in rice.

    abstract::The feasibility of using the FLP/FRT site-specific recombination system in rice for genome engineering was evaluated. Transgenic rice plants expressing the FLP recombinase were crossed with plants harbouring the kanamycin resistance gene (neomycin phosphotransferase II, nptII) flanked by FRT sites, which also served t...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2007.00310.x

    authors: Hu Q,Kononowicz-Hodges H,Nelson-Vasilchik K,Viola D,Zeng P,Liu H,Kausch AP,Chandlee JM,Hodges TK,Luo H

    更新日期:2008-02-01 00:00:00

  • Activity-based proteomics reveals nine target proteases for the recombinant protein-stabilizing inhibitor SlCYS8 in Nicotiana benthamiana.

    abstract::Co-expression of protease inhibitors like the tomato cystatin SlCYS8 is useful to increase recombinant protein production in plants, but key proteases involved in protein proteolysis are still unknown. Here, we performed activity-based protein profiling to identify proteases that are inhibited by SlCYS8 in agroinfiltr...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13092

    authors: Jutras PV,Grosse-Holz F,Kaschani F,Kaiser M,Michaud D,van der Hoorn RAL

    更新日期:2019-08-01 00:00:00

  • Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.).

    abstract::Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350 plant species. A few peanut cultivars were found to possess stable and durable bacterial wilt resistance (BWR). Genomics-assisted breeding can accelerate the process of developing resistant cultivars by using diagnostic marke...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13153

    authors: Luo H,Pandey MK,Khan AW,Wu B,Guo J,Ren X,Zhou X,Chen Y,Chen W,Huang L,Liu N,Lei Y,Liao B,Varshney RK,Jiang H

    更新日期:2019-12-01 00:00:00

  • Tuber-specific cphA expression to enhance cyanophycin production in potatoes.

    abstract::The production of biodegradable polymers that can be used to substitute petrochemical compounds in commercial products in transgenic plants is an important challenge for plant biotechnology. Nevertheless, it is often accompanied by reduced plant fitness. To decrease the phenotypic abnormalities of the sprout and to in...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2009.00451.x

    authors: Hühns M,Neumann K,Hausmann T,Klemke F,Lockau W,Kahmann U,Kopertekh L,Staiger D,Pistorius EK,Reuther J,Waldvogel E,Wohlleben W,Effmert M,Junghans H,Neubauer K,Kragl U,Schmidt K,Schmidtke J,Broer I

    更新日期:2009-12-01 00:00:00

  • Synthesis of bacteriophage lytic proteins against Streptococcus pneumoniae in the chloroplast of Chlamydomonas reinhardtii.

    abstract::There is a pressing need to develop novel antibacterial agents given the widespread antibiotic resistance among pathogenic bacteria and the low specificity of the drugs available. Endolysins are antibacterial proteins that are produced by bacteriophage-infected cells to digest the bacterial cell wall for phage progeny...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12703

    authors: Stoffels L,Taunt HN,Charalambous B,Purton S

    更新日期:2017-09-01 00:00:00