bims-plasge 2018-07-15 papers

on Plastid Genes

Issue of 2018‒07‒15
nine papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop.
SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis.
MORC domain definition and evolutionary analysis of the MORC gene family in green plants.
Identifying molecular markers suitable for Frl selection in tomato breeding.
Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae).
Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content.
Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.
A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India.
A role for plant science in underpinning the objective of global nutritional security?

Ann Bot. 2018 Jul 04.

Origin and parental genome characterization of the allotetraploid Stylosanthes scabra Vogel (Papilionoideae, Leguminosae), an important legume pasture crop.

André Marques, Lívia Moraes, Maria Aparecida Dos Santos, Iara Costa, Lucas Costa, Tomáz Nunes, Natoniel Melo, Marcelo F Simon, Andrew R Leitch, Cicero Almeida, Gustavo Souza.

Backgrounds and Aims: The genus Stylosanthes includes nitrogen-fixing and drought-tolerant species of considerable economic importance for perennial pasture, green manure and land recovery. Stylosanthes scabra is adapted to variable soil conditions, being cultivated to improve pastures and soils worldwide. Previous studies have proposed S. scabra as an allotetraploid species (2n = 40) with a putative diploid A genome progenitor S. hamata or S. seabrana (2n = 20) and the B genome progenitor S. viscosa (2n = 20). We aimed to provide conclusive evidence for the origin of S. scabra.Methods: We performed fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) experiments and Illumina paired-end sequencing of S. scabra, S. hamata and S. viscosa genomic DNA, to assemble and compare complete ribosomal DNA (rDNA) units and chloroplast genomes. Plastome- and genome-wide single nucleotide variation detection was also performed.
Key Results : GISH and phylogenetic analyses of plastid DNA and rDNA sequences support that S. scabra is an allotetraploid formed from 0.63 to 0.52 million years ago (Mya), from progenitors with a similar genome structure to the maternal donor S. hamata and the paternal donor S. viscosa. FISH revealed a non-additive number of 35S rDNA sites in S. scabra compared with its progenitors, indicating the loss of one locus from A genome origin. In S. scabra, most 5S rDNA units were similar to S. viscosa, while one 5S rDNA site of reduced size most probably came from an A genome species as revealed by GISH and in silico analysis.
Conclusions: Our approach combined whole-plastome and rDNA assembly with additional cytogenetic analysis to shed light successfully on the allotetraploid origin of S. scabra. We propose a Middle Pleistocene origin for S. scabra involving species with maternal A and paternal B genomes. Our data also suggest that variation found in rDNA units in S. scabra and its progenitors reveals differences that can be explained by homogenization, deletion and amplification processes that have occurred since its origin.

DOI: https://doi.org/10.1093/aob/mcy113
Nucleic Acids Res. 2018 Jun 30.

SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis.

Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu.

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEAD-box pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences pri-miRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also enhances the abundance of the DCL1 protein levels through promoting the splicing of the DCL1 pre-mRNAs. Collectively, our data provide new insights into the function of SMA1/Prp28 in regulating miRNA abundance in plants.

DOI: https://doi.org/10.1093/nar/gky591
Genome Biol Evol. 2018 Jul 02.

MORC domain definition and evolutionary analysis of the MORC gene family in green plants.

Wei Dong, Alessandro Vannozzi, Fei Chen, Yue Hu, Zihua Chen, Liangsheng Zhang.

Microrchidia (MORC) proteins have been described as epigenetic regulators and plant immune mediators in Arabidopsis. Typically, plant and animal MORC proteins contain a hallmark GHKL-type (Gyrase, Hsp90, Histidine kinase, MutL) ATPase domain in their N-terminus. Here, 356 and 83 MORC orthologues were identified in 60 plant and 27 animal genomes. Large-scale MORC sequence analyses revealed the presence of a highly conserved motif composition that defined as the MORC domain. The MORC domain was present in both plants and animals, indicating that it originated in the common ancestor before the divergence of plants and animals. Phylogenetic analyses showed that MORC genes in both plant and animal lineages were clearly classified into two major groups, named Plants-Group I, Plants-Group II and Animals-Group I, Animals-Group II, respectively. Further analyses of MORC genes in green plants uncovered that Group I can be subdivided into Group I-1 and Group I-2. Group I-1 only contains seed plant genes, suggesting that Group I-1 and I-2 divergence occurred at least before the emergence of spermatophytes. Group I-2 and Group II have undergone several gene duplications, resulting in the expansion of MORC gene family in angiosperms. Additionally, MORC gene expression analyses in Arabidopsis, soybean, and rice revealed a higher expression level in reproductive tissues compared to other organs, and showed divergent expression patterns for several paralogous gene pairs. Our studies offered new insights into the origins, phylogenetic relationships, and expressional patterns of MORC family members in green plants, which would help to further reveal their functions as plant epigenetic regulators.

DOI: https://doi.org/10.1093/gbe/evy136
Theor Appl Genet. 2018 Jul 07.

Identifying molecular markers suitable for Frl selection in tomato breeding.

Zübeyir Devran, Erdem Kahveci, Yiguo Hong, David J Studholme, Mahmut Tör.

Modern plant breeding heavily relies on the use of molecular markers. In recent years, next generation sequencing (NGS) emerged as a powerful technology to discover DNA sequence polymorphisms and generate molecular markers very rapidly and cost effectively, accelerating the plant breeding programmes. A single dominant locus, Frl, in tomato provides resistance to the fungal pathogen Fusarium oxysporum f. sp. radicis-lycopersici (FORL), causative agent of Fusarium crown and root rot. In this study, we describe the generation of molecular markers associated with the Frl locus. An F2 mapping population between an FORL resistant and a susceptible cultivar was generated. NGS technology was then used to sequence the genomes of a susceptible and a resistant parent as well the genomes of bulked resistant and susceptible F2 lines. We zoomed into the Frl locus and mapped the locus to a 900 kb interval on chromosome 9. Polymorphic single-nucleotide polymorphisms (SNPs) within the interval were identified and markers co-segregating with the resistant phenotype were generated. Some of these markers were tested successfully with commercial tomato varieties indicating that they can be used for marker-assisted selection in large-scale breeding programmes.

DOI: https://doi.org/10.1007/s00122-018-3136-0
Mol Phylogenet Evol. 2018 Jul 04. pii: S1055-7903(17)30942-9. [Epub ahead of print]

Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae).

Wen-Qing Ye, Zhao-Yan Yap, Pan Li, Hans Peter Comes, Ying-Xiong Qiu.

  Species of Podophylloideae (Berberidaceae, Ranunculales) are of great pharmacogenetic importance and represent the classic biogeographic disjunction between eastern Asia (EA; 10 ssp.) and eastern North America (ENA; 2 ssp.). However, previous molecular studies of this group suffered from low phylogenetic resolution and/or insufficient marker variability. This study is the first to report whole-plastome sequence data for all 12 species of Podophylloideae (14 individuals) and a close relative, Achlys triphylla. These 15 plastomes proved highly similar in overall size (156,240-157,370 bp), structure, gene order and content, also when compared to other Ranunculales, but also revealed some structural variations caused by the expansion or contraction of the inverted repeats (IRs) into or out of adjacent single-copy regions. Our phylogenomic analysis, based on 63 plastome-derived protein-coding genes (CDS), supported the monophyly of Podophylloideae and its two major genera (EA: Dysosma, EA/ENA: Diphylleia), with Podophyllum peltatum L. (ENA) being more closely related to Diphylleia than to the group's earliest diverging species, Sinopodophyllum hexandrum (EA). Furthermore, within this subfamily/dataset, matK was identified as the fastest evolving gene, which proved to be under positive selection especially in more recently derived, lower-elevation lineages of Dysosma, possibly reflecting an adaptive response to novel environmental (i.e. subtropical compared to higher-elevation/alpine) conditions. Finally, several highly variable noncoding regions were identified in the plastomes of Podophylloideae and Ranunculales. These highly variable loci should be the best choices for future phylogenetic, phylogeographic, and population-level genetic studies. Overall, our results demonstrate the power of plastid phylogenomics to improve phylogenetic resolution, and contribute to a better understanding of plastid gene evolution in Podophylloideae.

Keywords:  Podophylloideae; adaptive evolution; genome structure; phylogeny; plastome

DOI:  https://doi.org/10.1016/j.ympev.2018.07.001
Plant Physiol Biochem. 2018 Jun 18. pii: S0981-9428(18)30269-9. [Epub ahead of print]130 112-126

Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content.

Jing Xia, Yan Jun Ma, Yue Wang, Jian Wen Wang.

  To investigate on the effects of autopolyploidization on growth and artemisinin biosynthesis in Artemisia annua, we performed a comprehensive transcriptomic characterization of diploid and induced autotetraploid A. annua. The polyploidization treatment not only enhanced photosynthetic capacity and endogenous contents of indole-3-acetic acid (IAA), abscisic acid (ABA) and jasmonic acid (JA), oxidative stress, but increased the average level of artemisinin in tetraploids from 42.0 to 63.6%. The obvious phenotypic alterations in tetraploids were observed including shorter stems, larger size of stomata and glandular secretory trichomes (GSTs), larger leaves, more branches and roots. A total of 8763 (8.85%) differentially expressed genes (DEGs) were identified in autotetraploids and mainly involved in carbohydrate metabolic processes, cell wall organization and defense responses. Both the up-regulated expression of DNA methylation unigenes and enhanced level of DNA methylation in autotetraploids indicated a possible role of DNA methylation on transcriptomic remodeling and phenotypic alteration. The up-regulated genes were enriched in response to extracellular protein biosynthesis, photosynthesis and hormone stimulus for cell enlargement and phenotypic alteration. The genomic shock induced by chromosome duplication stimulated the expression of transcripts related to oxidative stress, biosynthesis and signal transduction of ABA and JA, and key enzymes in artemisinin biosynthetic pathway, leading to the increased accumulation of artemisinin. This is the first transcriptomic research that identifies DEGs involved in the polyploidization of A. annua. The results provide novel information for understanding the complexity of polyploidization and for further identification of the factors and genes involve in artemisinin biosynthesis.

Keywords:  Artemisia annua L.; Artemisinin biosynthesis; Autopolyploidy; Phenotypic alteration; Transcriptome

DOI:  https://doi.org/10.1016/j.plaphy.2018.06.018
DNA Res. 2018 Jun 29.

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Satoshi Takahashi, Kenji Osabe, Naoki Fukushima, Shohei Takuno, Naomi Miyaji, Motoki Shimizu, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Elizabeth S Dennis, Motoaki Seki, Ryo Fujimoto.

Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant's phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24 nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24 nt siRNAs and H3K9me2 are discussed.

DOI: https://doi.org/10.1093/dnares/dsy021
Database (Oxford). 2018 Jan 01. 2018

A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India.

Kabita Tripathy, Balwant Singh, Nisha Singh, Vandna Rai, Gauri Misra, Nagendra Kumar Singh.

Rice is a staple food for the people of Asia that supplies more than 50% of the food energy globally. It is widely accepted that the crop domestication process has left behind substantial useful genetic diversity in their wild progenitor species that has huge potential for developing crop varieties with enhanced resistance to an array of biotic and abiotic stresses. In this context, Oryza rufipogon, Oryza nivara and their intermediate types wild rice germplasm/s collected from diverse agro-climatic regions would provide a rich repository of genes and alleles that could be utilized for rice improvement using genomics-assisted breeding. Here we present a database of detailed information on 614 such diverse wild rice accessions collected from different agro-climatic zones of India, including 46 different morphological descriptors, complete passport data and DNA fingerprints. The information has been stored in a web-based database entitled 'Indian Wild Rice (IWR) Database'. The information provided in the IWR Database will be useful for the rice geneticists and breeders for improvement of rice cultivars for yield, quality and resilience to climate change.Database URL: http://nksingh.nationalprof.in: 8080/iwrdb/index.jsp.

DOI: https://doi.org/10.1093/database/bay058
Ann Bot. 2018 Jul 06.

A role for plant science in underpinning the objective of global nutritional security?

Cathie Martin.

Background: The challenges of achieving global food security have become more demanding as scientists have realized that not only calorie content but also food composition and colonic microbial content impact our health and well-being, dramatically. The ways that the nutrients we consume affect our health are highly complex due to the diversity of what we eat, the varying digestibility of what we eat, the changing composition and functioning of each individual's gut microbiota, the differences in absorption and bioavailability of the nutrients we eat, the differences in responses between individuals to what they eat and the multi-fold mechanisms of action that nutrients have on our health.Perspective and Conclusions: It has been accepted for more than 50 years that diets rich in plants, particularly fruit and vegetables, protect health, and yet such diets have declined, with lower fruit and vegetable content and much more cheap, sugary, oily, processed foods, over the same period. These dietary shifts have had a marked impact on the incidence of chronic diseases: obesity, metabolic diseases, type 2 diabetes and cardiovascular diseases. Greater support for research into the ways that plant-based foods impact health will be essential for changing dietary patterns to protect health and to achieve global nutritional security.

DOI: https://doi.org/10.1093/aob/mcy118