bims-plasge 2018-06-03 papers

on Plastid Genes

Issue of 2018‒06‒03
six papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Genetic analysis of yield and agronomic traits under reproductive stage drought stress in rice using a high-resolution linkage map.
The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae.
Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).
Diversity of Organellar Genomes in Non-photosynthetic Diatoms.
Structural Flexibility Enables Alternative Maturation, ARGONAUTE Sorting and Activities of miR168, a Global Gene Silencing Regulator in Plants.
Unbuttoning the ancestral flower of angiosperms.

Gene. 2018 May 23. pii: S0378-1119(18)30583-3. [Epub ahead of print]

Genetic analysis of yield and agronomic traits under reproductive stage drought stress in rice using a high-resolution linkage map.

Uttam Bhattarai, Prasanta K Subudhi.

  Drought stress at the reproductive stage of rice crop leads to huge loss in grain yield. Identification and introgression of large effect drought tolerant QTLs are necessary to develop drought tolerant rice varieties. Compared to the high-density linkage maps, widely spaced markers lead to identification of QTLs with large confidence intervals which are difficult to incorporate in a breeding program. A previously generated genotyping-by-sequencing (GBS) based linkage map consisting of 4748 SNP markers was used to map QTLs in Cocodrie × N-22 recombinant inbred line (RIL) population. Twenty-one QTLs were discovered for days to flowering (DTF), plant height (PH), leaf rolling score (LRS), plant dry matter content (DM), spikelet fertility (SF), grain yield (GY), yield index (YI), and harvest index (HI) under drought stress. A major QTL qPH1.38 was identified in a narrow confidence interval on chromosome 1. The QTLs, qDTF3.01 and qPH1.38, overlapped with the previously identified QTL qDTY1.1 and Hd9, respectively. Another large-effect QTL qLRS1.37 was identified close to the sd1 locus on chromosome 1. A grain yield QTL qGY1.42 located on chromosome 1 contained only 4 candidate genes. There was no overlapping of QTLs for the root traits and the yield attributes. The important candidate genes present within the large effect QTL regions are MYB transcription factors, no apical meristem protein (NAC), potassium channel protein, nuclear matrix protein1, and chlorophyll A-B binding protein. The large effect QTLs (qDTF3.01, qPH1.38, and qLRS1.37) and a novel grain yield QTL qGYS1.42 can be used to incorporate in elite breeding lines to develop drought-tolerant rice varieties.

Keywords:  Candidate genes; Genotyping by sequencing (GBS); QTL mapping; Recombinant inbred lines; Reproductive stage; Single nucleotide polymorphism

DOI:  https://doi.org/10.1016/j.gene.2018.05.086
Gene. 2018 May 23. pii: S0378-1119(18)30584-5. [Epub ahead of print]

The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae.

Amanda de Santana Lopes, Túlio Gomes Pacheco, Leila do Nascimento Vieira, Miguel Pedro Guerra, Rubens Onofre Nodari, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa, Marcelo Rogalski.

  Crambe abyssinica is an important oilseed crop that accumulates high levels of erucic acid, which is being recognized as a potential oil platform for several industrial purposes. It belongs to the family Brassicaceae, assigned within the tribe Brassiceae. Both family and tribe have been the subject of several phylogenetic studies, but the relationship between some lineages and genera remains unclear. Here, we report the complete sequencing and characterization of the C. abyssinica plastome. Plastome structure, gene order, and gene content of C. abyssinica are similar to other species of the family Brassicaceae. The only exception is the rps16 gene, which is absent in many genera within the family Brassicaceae, but seems to be functional in the tribe Brassiceae, including C. abyssinica. However, the analysis of gene divergence shows that the rps16 is the most divergent gene in C. abyssinica and within the tribe Brassiceae. In addition, species of the tribe Brassiceae also show similar SSR loci distribution, with some regions containing a high number of SSRs, which are located mainly at the single copy regions. Six hotspots of nucleotide divergence among Brassiceae species were located in the single copy regions by sliding window analysis. Brassicaceae phylogenomic analysis, based on the complete plastomes of 72 taxa, resulted in a well-supported and well-resolved tree. The genus Crambe is positioned within the Brassiceae clade together with the genera Brassica, Raphanus, Sinapis, Cakile, Orychophragmus and Sinalliaria. Moreover, we report several losses and gains of RNA editing sites that occurred in plastomes of Brassiceae species during evolution.

Keywords:  Extranuclear inheritance; Gene function; Genetic divergence; Oilseeds; Organellar DNA; Plastid molecular markers

DOI:  https://doi.org/10.1016/j.gene.2018.05.088
Mol Phylogenet Evol. 2018 May 24. pii: S1055-7903(17)30744-3. [Epub ahead of print]

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea).

Charles S P Foster, Murray J Henwood, Simon Y W Ho.

  Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics.

Keywords:  Molecular systematics; Pimelea; chloroplast genome; monophyly; phylogenetic clustering; riceflowers

DOI:  https://doi.org/10.1016/j.ympev.2018.05.018
Protist. 2018 Apr 27. pii: S1434-4610(18)30033-6. [Epub ahead of print]169(3): 351-361

Diversity of Organellar Genomes in Non-photosynthetic Diatoms.

Ryoma Kamikawa, Tomonori Azuma, Ken-Ichiro Ishii, Yusei Matsuno, Hideaki Miyashita.

  We determined the complete sequences of the plastid and mitochondrial genomes of three non-photosynthetic Nitzschia spp., as well as those of a photosynthetic close relative, Nitzschia palea. All the plastid genomes and the three mitochondrial genomes determined were found to be circularly mapping, and the other mitochondrial genomes were predicted to be of a linear form with telomere-like structures at both ends. We found that all the non-photosynthetic plastid genomes are streamlined and lack a common gene set: two RNA genes, and 60 protein-coding genes, most of which are related to photosynthetic functions. Nevertheless, the non-photosynthetic plastid genomes commonly retain ATP synthase complex genes, although atpE is missing in Nitzschia sp. NIES-3581 and three other non-photosynthetic species lack atpF instead of atpE. This observation suggests an evolutionary constraint against the loss of ATP synthase complex genes. All the non-photosynthetic diatom plastid genomes lacked two genes, thiS and thiG, involved in thiamin biosynthesis. Consistent with this gene loss, non-photosynthetic Nitzschia spp. were incapable of thriving in vitamin B1-lacking media. This study clearly demonstrated not only the evolutionary trends of plastid genome reduction but also the linkage between plastid genome reduction and a biological change of nutrient requirements in Nitzschia.

Keywords:  ATP synthase complex; Nitzschia; mitochondria; plastids; vitamin B1.

DOI:  https://doi.org/10.1016/j.protis.2018.04.009
Mol Plant. 2018 May 24. pii: S1674-2052(18)30165-5. [Epub ahead of print]

Structural Flexibility Enables Alternative Maturation, ARGONAUTE Sorting and Activities of miR168, a Global Gene Silencing Regulator in Plants.

Taichiro Iki, Cléry Antoine, Nicolas Bologna, Alexis Sarazin, Christopher Brosnan, Nathan Pumplin, Frédéric H T Allain, Olivier Voinnet.

  In eukaryotes, the RNase-III Dicer often produces length/sequence microRNA (miRNA) variants, called "isomiRs", owing to intrinsic structural/sequence determinants of miRNA precursors (pre-miRNAs). Here, we combined biophysics, genetics and biochemistry to study Arabidopsis miR168, the key feedback-regulator of the central plant silencing effector protein ARGONAUTE1 (AGO1). We identified a motif conserved among plant pre-miR168 orthologs that enables flexible internal base-pairing underlying at least three metastable structural configurations. These promote alternative, accurate Dicer cleavage generating length and structural isomiR168 variants with distinctive AGO sorting properties and modes of action. Among these isomiR168s, a duplex with a 22-nt guide-strand exhibits strikingly preferential affinity for AGO10, the closest AGO1 paralog. The 22-nt miR168-AGO10 complex antagonizes AGO1 accumulation including via "transitive RNAi", a silencing-amplification process maintaining appropriate AGO1 cellular homeostasis. We further show how the tombusviral P19 silencing-suppressor protein displays markedly weaker affinity for the 22-nt form among its isomiR168 cargoes, thereby promoting AGO10-directed suppression of AGO1-mediated antiviral silencing. We conclude that structural flexibility, a so far overlooked property of pre-miRNAs, considerably increases the versatility and regulatory potential of individual MIRNA genes, and that pathogens have evolved to usurp this property.

Keywords:  P19; Plants; isoforms/ structural flexibility/ Dicer/ ARGONAUTE; miR168; microRNA; sorting; tombusvirus

DOI:  https://doi.org/10.1016/j.molp.2018.05.006
Trends Plant Sci. 2018 May 24. pii: S1360-1385(18)30113-4. [Epub ahead of print]

Unbuttoning the ancestral flower of angiosperms.

Orlando C De-Paula, Leandro C S Assis, Louis P Ronse de Craene.

  A recent study using an extensive data set plus sophisticated analytical tools reconstructed a model of the ancestral angiosperm flower. Although attractive, it presents problems of homology assessment. We discuss its inconsistencies and endorse the use of a comparative model that integrates biological parameters as essential to elucidate floral evolution.

Keywords:  floral development; floral evolution; floral vascularisation; gene expression; homology assessment; phyllotaxis

DOI:  https://doi.org/10.1016/j.tplants.2018.05.006