bims-plasge 2019-04-14 papers

on Plastid genes

Issue of 2019‒04‒14
seven papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Pacbio Sequencing Reveals Identical Organelle Genomes between American Cranberry (Vaccinium macrocarpon Ait.) and a Wild Relative.
Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.).
Mapping-by-sequencing using NGS-based 3'-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.).
Organellar DNA Polymerases in Complex Plastid-Bearing Algae.
Unravelling hidden components of the chloroplast envelope proteome: opportunities and limits of better MS sensitivity.
Linkage mapping and GWAS reveal candidate genes conferring thermotolerance of seed-set in maize.
A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum.

Genes (Basel). 2019 Apr 10. pii: E291. [Epub ahead of print]10(4):

Pacbio Sequencing Reveals Identical Organelle Genomes between American Cranberry (Vaccinium macrocarpon Ait.) and a Wild Relative.

Luis Diaz-Garcia, Lorraine Rodriguez-Bonilla, Jessica Rohde, Tyler Smith, Juan Zalapa.

  Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry, and could be useful to improve fruit quality such as phytochemical content. Furthermore, given their northern distribution, they could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, the Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos.

Keywords:  American cranberry; Vaccinium; domestication; organelle genomes

DOI:  https://doi.org/10.3390/genes10040291
Int J Mol Sci. 2019 Apr 10. pii: E1773. [Epub ahead of print]20(7):

Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.).

Eliška Nováková, Lenka Zablatzká, Jan Brus, Viktorie Nesrstová, Pavel Hanáček, Ruslan Kalendar, Fatima Cvrčková, Ľuboš Majeský, Petr Smýkal.

  Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.

Keywords:  acetyl-CoA carboxylase; hybrid incompatibility; hybrid necrosis; nuclear-cytoplasmic conflict; pea; reproductive isolation; speciation

DOI:  https://doi.org/10.3390/ijms20071773
PeerJ. 2019 ;7 e6662

Mapping-by-sequencing using NGS-based 3'-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.).

Aleksandr I Zhernakov, Oksana Y Shtark, Olga A Kulaeva, Jaroslava V Fedorina, Alexey M Afonin, Anna B Kitaeva, Viktor E Tsyganov, Fabian Afonso-Grunz, Klaus Hoffmeier, Björn Rotter, Peter Winter, Igor A Tikhonovich, Vladimir A Zhukov.

  Large collections of pea symbiotic mutants were accumulated in the 1990s, but the causal genes for a large portion of the mutations are still not identified due to the complexity of the task. We applied a Mapping-by-Sequencing approach including Bulk Segregant Analysis and Massive Analysis of cDNA Ends (MACE-Seq) sequencing technology for genetic mapping the Sym11 gene of pea which controls the formation of symbioses with both nodule bacteria and arbuscular-mycorrhizal fungi. For mapping we developed an F 2-population from the cross between pea line N24 carrying the mutant allele of sym11 and the wild type NGB1238 (=JI0073) line. Sequencing libraries were prepared from bulks of 20 plants with mutant and 12 with wild-type phenotype. MACE-Seq differential gene expression analysis between mutant-phenotype and wild-type-phenotype bulks revealed 2,235 genes, of which 514 (23%) were up-regulated and 1,721 (77%) were down-regulated in plant roots inoculated with rhizobia as a consequence of sym11 mutation. MACE-Seq also detected single nucleotide variants between bulks in 217 pea genes. Using a novel mathematical model we calculated the recombination frequency (RF) between the Sym11 gene and these 217 polymorphic genes. Six genes with the lowest RF were converted into CAPS or dCAPS markers and genetically mapped on the complete mapping population of 108 F 2-plants which confirmed their tight linkage to Sym11 and to each other. The Medicago truncatula Gaertn. (Mt) homologs of these genes are located in a distinct region of Mt chromosome 5, which corresponds to linkage group I of pea. Among 94 candidate genes from this region only one was down-regulated-the pea Sym33 homolog of the Mt IPD3 gene which is essential for nodulation. Sequencing of the Sym33 allele of the N24 (sym11) mutant revealed a single nucleotide deletion (c.C319del) in its third exon resulting in a codon shift in the open reading frame and premature translation termination. Thus, we identified a novel mutant allele sym33-4 most probably responsible for the mutant phenotype of the N24 (sym11) line, thereby demonstrating that mapping by MACE-Seq can be successfully used for genetic mapping of mutations and identification of candidate genes in pea.

Keywords:  Mapping-by-sequencing; Massive analysis of cDNA Ends; Next generation sequencing; Pea; RNA-Seq; Symbiotic genes

DOI:  https://doi.org/10.7717/peerj.6662
Biomolecules. 2019 04 07. pii: E140. [Epub ahead of print]9(4):

Organellar DNA Polymerases in Complex Plastid-Bearing Algae.

Yoshihisa Hirakawa, Arisa Watanabe.

  DNA replication in plastids and mitochondria is generally regulated by nucleus-encoded proteins. In plants and red algae, a nucleus-encoded enzyme called POP (plant and protist organellar DNA polymerase) is involved in DNA replication in both organelles by virtue of its dual localization. POPs are family A DNA polymerases, which include bacterial DNA polymerase I (PolI). POP homologs have been found in a wide range of eukaryotes, including plants, algae, and non-photosynthetic protists. However, the phylogeny and subcellular localizations of POPs remain unclear in many algae, especially in secondary and tertiary plastid-bearing groups. In this study, we report that chlorarachniophytes possess two evolutionarily distinct POPs, and fluorescent protein-tagging experiments demonstrate that they are targeted to the secondary plastids and mitochondria, respectively. The timing of DNA replication is different between the two organelles in the chlorarachniophyte Bigelowiella natans, and this seems to be correlated to the transcription of respective POP genes. Dinoflagellates also carry two distinct POP genes, possibly for their plastids and mitochondria, whereas haptophytes and ochrophytes have only one. Therefore, unlike plants, some algal groups are likely to have evolved multiple DNA polymerases for various organelles. This study provides a new insight into the evolution of organellar DNA replication in complex plastid-bearing organisms.

Keywords:  DNA replication; algae; chlorarachniophytes; endosymbiosis; mitochondria; plastids

DOI:  https://doi.org/10.3390/biom9040140
Mol Cell Proteomics. 2019 Apr 08. pii: mcp.RA118.000988. [Epub ahead of print]

Unravelling hidden components of the chloroplast envelope proteome: opportunities and limits of better MS sensitivity.

Imen Bouchnak, Sabine Brugière, Lucas Moyet, Sophie Le Gall, Daniel Salvi, Marcel Kuntz, Marianne Tardif, Norbert Rolland.

  The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides…) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast sub-compartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared to the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.

Keywords:  Cell fractionation*; Cellular organelles*; Chloroplast; Chloroplast envelope; Plant Biology*; Subcellular Separation; Subcellular analysis

DOI:  https://doi.org/10.1074/mcp.RA118.000988
J Exp Bot. 2019 Apr 11. pii: erz171. [Epub ahead of print]

Linkage mapping and GWAS reveal candidate genes conferring thermotolerance of seed-set in maize.

Jingyang Gao, Songfeng Wang, Zijian Zhou, Shiwei Wang, Chaopei Dong, Cong Mu, Yunxia Song, Peipei Ma, Chengcheng Li, Zhao Wang, Kewei He, Chunyan Han, Jiafa Chen, Haidong Yu, Jianyu Wu.

  High temperature stress (HS) will increasingly affect crop yield worldwide. In order to determine the genetic basis of thermotolerance of seed-set in maize in field conditions, a QTL mapping in a recombinant inbred line (RIL) population was performed using a collection of 8329 high-density single nucleotide polymorphisms (SNP) markers developed in this study, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259,973 SNPs. In total, 4 quantitative trait loci (QTLs) and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified by linkage mapping and GWAS, respectively. Four candidate genes among them were found in both linkage mapping and GWAS. Thermotolerance on seed-set were increased significantly in the near-isogenic lines (NILs) incorporating the four candidate genes in a susceptible parent background. Moreover, the expression profiles of two of the four candidate genes showed that they were induced by high temperature in maize tassel in the tolerant parent background. These genetic analyses indicated that thermotolerance of maize seed-set is regulated by multiple genes with minor effect, in which calcium signaling plays a core role. The pyramiding breeding with beneficial alleles and candidate genes could improve seed-set and yield of maize under HS.

Keywords:  Calcium signaling; GWAS; candidate genes; high temperature stress; high-density SNP markers; linkage mapping; maize; seed-set; thermotolerance

DOI:  https://doi.org/10.1093/jxb/erz171
PLoS One. 2019 ;14(4): e0215175

A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum.

Beata I Czajkowska, Hugo R Oliveira, Terence A Brown.

The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1, Ppd-B1 and Ppd-G1 genes from multiple accessions of T. turgidum and T. timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1. We used these PCRs with 51 accessions of T. timopheevii and 20 of T. turgidum. Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T. turgidum were identified as T. timopheevii by the PCRs, and one T. timopheevii accession was typed as T. turgidum. We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T. turgidum and T. timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene.

DOI: https://doi.org/10.1371/journal.pone.0215175