Geographic patterns of histone H1 allelic frequencies formed in the course of Pisum sativum L. (pea) cultivation

New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)

Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.

A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection

Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs. These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of accessions from Central Asia appear nearly as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. PSPPC genotypes can be paired with new and existing phenotype data for trait mapping; as proof-of-concept, we localized Mendel's A gene controlling flower color to its known position. We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. Taken together, the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5–20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Divergence and population traits in evolution of the genus Pisum L. as reconstructed using genes of two histone H1 subtypes showing different phylogenetic resolution

Two histone H1 subtype genes, His7 and His5, were sequenced in a set of 56 pea accessions. Phylogenetic reconstruction based on concatenated His5 and His7 sequences had three main clades. First clade corresponded to Pisum fulvum, the next divergence separated a clade inside Pisum sativum in the broad sense that did not correspond strictly to any proposed taxonomical subdivisions. According to our estimations, the earliest divergence separating P. fulvum occurred 1.7±0.4MYA. The other divergence with high bootstrap support that separated two P. sativum groups took place approximately 1.3±0.3MYA. Thus, the main divergences in the genus took place either in late Pliocene or in early Pleistocene, the time of onset of the profound climate cooling in the northern hemisphere. The ω=K(a)/K(s) ratio was 2.5 times higher for His5 sequences than for His7. Thus, His7 gene, coding for a unique subtype specific for actively growing tissues, might have evolved under stricter evolutionary constraints than His5, that codes for a minor H1 subtype with less specific expression pattern. For this reason phylogenetic reconstructions separately obtained from His5 sequences resolved tree topology much better than those obtained from His7 sequences. Computational estimation of population dynamic parameters in the genus Pisum L. from His5-His7 sequences using IMa2 software revealed a decrease of effective population size on the early stage of Pisum evolution.

Linker histone subtypes and their allelic variants

Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance.

Polymorphism in a histone H1 subtype with a short N-terminal domain in three legume species (Fabaceae, Fabaeae)

A number of alleles of an orthologous gene His6 encoding histone H1 subtype f (H1-6 in pea) accumulated in chromatin of old tissues were sequenced in three legume species: seven alleles in Pisum sativum, four in Vicia unijuga and eight in Lathyrus gmelinii. In the total of 19 alleles sequenced in the three species, 29 non-synonymous substitutions and six indels were found in the coding region; most of amino acid substitutions (26 of 29) and all indels occurred in the C-terminal hydrophilic domain of the encoded protein. All species were polymorphic for some non-synonymous substitutions, V. unijuga was also polymorphic for one and P. sativum for two indels. Three near-isogenic lines of P. sativum bearing different alleles showed differences in many quantitative traits; that in the growth dynamic could be tentatively attributed to the allelic substitution of subtype H1-6. The frequencies of four electromorphs in a sampled locality of V. unijuga were found to be close to those observed 25 years ago, although their rapid change in the past was supposed in the previous study.

Phylogenetic reconstruction at the species and intraspecies levels in the genus Pisum (L.) (peas) using a histone H1 gene

A phylogenetic analysis of the genus Pisum (peas), embracing diverse wild and cultivated forms, which evoke problems with species delimitation, was carried out based on a gene coding for histone H1, a protein that has a long and variable functional C-terminal domain. Phylogenetic trees were reconstructed on the basis of the coding sequence of the gene His5 of H1 subtype 5 in 65 pea accessions. Early separation of a clear-cut wild species Pisum fulvum is well supported, while cultivated species Pisum abyssinicum appears as a small branch within Pisum sativum. Another robust branch within P. sativum includes some wild and almost all cultivated representatives of P. sativum. Other wild representatives form diverse but rather subtle branches. In a subset of accessions, PsbA-trnH chloroplast intergenic spacer was also analysed and found less informative than His5. A number of accessions of cultivated peas from remote regions have a His5 allele of identical sequence, encoding an electrophoretically slow protein product, which earlier attracted attention as likely positively selected in harsh climate conditions. In PsbA-trnH, a 8bp deletion was found, which marks cultivated representatives of P. sativum.

Geographic patterns of histone H1 encoding genes allelic variation in Aegilops tauschii Coss. (Poaceae)

An electrophoretic analysis of histone H1 of Aegilops tauschii was carried out using the collection of 303 accessions (156 of ssp. tauschii and 147 of ssp. stangulata) representing all the species range. Three, four and six allelic variants were found for Hst1, Hst2 and Hst3 locus, respectively. The level of histone H1 allelic variability in ssp. strangulata was considerably higher than in ssp. tauschii. Expected heterozygosity (H(E)) for the loci Hst1, Hst2 and Hst3 made up 0.066, 0.484 and 0.224 respectively in ssp. strangulata vs. 0.024, 0.051 and 0.214 in ssp. tauschii. Besides the most common haplotype, Hst1 (1000), Hst2 (1000), Hst3 (1000), five other haplotypes with frequencies of occurrence higher than 0.02 were found in ssp. strangulata, and only one such haplotype--in ssp. tauschii. The most part of histone H1 variation in ssp. tauschii was in the western part of the area. In ssp. strangulata, the alleles Hst2 (988) and Hst2 (973) were found only in Caucasia, and the allele Hst1 (1043)--only in Precaspian Iran and south-eastern Azerbaijan. Histone H1 variation patterns in Ae. tauschii are very similar to those of non-coding sequences of chloroplast DNA. Therefore, histone H1 allelic variation in this species seems to be mostly neutral. Nevertheless, the evidences were pointed out, revealing that some part of variation at Hst2 locus in ssp. strangulata could be adaptive. It seems that Hst2 (1026) allele is disadvantageous in western Precaspian Iran, the region with the high annual rainfall, and being eliminated by natural selection.

Phenotypic effect of substitutions of short chromosomal segments containing different alleles of histone HI genes in garden pea (Pisum sativum L.)

A hypothesis has been tested that alterations in the molecule of histone H1 are capable of influencing quantitative traits of an organism. Two pairs of isogenic lines were constructed by selfing of plants kept heterozygous either for allelic variants of histone H1 subtype 1 (His1 gene) or for allelic combinations (haplotypes) of closely linked genes of H1 subtypes 3, 4, 5 and 6 (gene cluster His(2–6)). After 19 and 15 generations of selfing, respectively, expectation of the length of chromosome which remained heterozygous has comprised 2·6 cM near Hisl and 3·5 cM near His(2–6). The third pair of isogenic lines was obtained as a result of two successive intracluster cross-over events bordering the gene of the subtype 5 (His5). In each pair of isogenic lines there have been revealed some statistically significant differences between mean values of a number of quantitative traits.

Phenotypic effect of substitution of allelic variants for a histone H1 subtype specific for growing tissues in the garden pea (Pisum sativum L.)

In pea, subtype H1-7 of histone H1 is specific for young actively growing tissues and disappears from chromatin of mature tissues. We sequenced the alleles coding for three main variants, numbered according to the increase of the electrophoretic mobility. Allele 1 differs from the most common allele 2 by eight nucleotide substitutions, two of them associated with amino acid replacements, His->Tyr in the globular domain and Ala->Val in the C-terminal domain. Allele 3 differs from alleles 1 and 2 by a 24-bp deletion in the part coding for the C-terminal domain. In three greenhouse experiments, we compared quantitative traits in nearly isogenic lines differing by these H1-7 variants. In experiment 1, three lines bearing either of the three allelic variants were compared, the other experiments involved pairs of lines bearing variants 1 and 3. In all experiments, statistically significant differences between the lines were registered, mostly related to the plant size. The most prominent effect was associated with plant growth dynamics. Plants of line 3, carrying the 8-amino acid deletion in histone H1-7, on average grew slower. In two experiments, the differences of the mean stem length persisted throughout plant growth while in experiment 2 differences disappeared upon maturity. The H1-7 subtype is supposed to be related to maintenance of chromatin state characteristic for cell growth and division.

Sequence variants of chicken linker histone H1.a

Two allelic isoforms (H1.a1 and H1.a2) of histone H1.a were identified within two conservative flocks (R11 and R55) of Rhode Island Red chickens. These proteins form three phenotypes: a1, a2 and a1a2. Birds with phenotype a1 were most common (frequency 0.825-0.980) while the a1a2 chickens appeared relatively rarely (0.017-0.175). The third phenotype a2, not detected in the tested populations, has only been revealed in progeny of the purpose-mated a1a2 birds. The polymorphism of histone H1.a was observed in all examined chicken tissues, so that the H1 preparations isolated from the lung, spleen, kidney and testis from the same individual exhibited identical phenotypes (a1, a2, or a1a2). This finding, together with inheritance data, supports the genetic nature of the H1.a polymorphism. As indicated by cleavages with alpha-chymotrypsin and protease V8, the H1.a1 and H1.a2 are two highly related proteins which differ within N-terminal part of their C-terminal tails. Only a single nonconservative amino acid substitution between both H1.a allelic isoforms was detected by Edman degradation: glutamic acid present at position 117 in histone H1.a1 was replaced by lysine in histone H1.a2. Furthermore, using microsequencing techniques we have found a sequence homology between the N- and C-terminal parts of an unknown minor protein H1.y, present in the phenotype a2, and similar regions of histone H1.b.

Structure of allelic variants of subtype 5 of histone H1 in pea Pisum sativum L

The pea genome contains seven histone H1 genes encoding different subtypes. Previously, the DNA sequence of only one gene, His1, coding for the subtype H1-1, had been identified. We isolated a histone H1 allele from a pea genomic DNA library. Data from the electrophoretic mobility of the pea H1 subtypes and their N-bromosuccinimide cleavage products indicated that the newly isolated gene corresponded to the H1-5 subtype encoded by His5. We confirmed this result by sequencing the gene from three pea lines with H1-5 allelic variants of altered electrophoretic mobility. The allele of the slow H1-5 variant differed from the standard allele by a nucleotide substitution that caused the replacement of the positively charged lysine with asparagine in the DNA-interacting domain of the histone molecule. A temperature-related occurrence had previously been demonstrated for this H1-5 variant in a study on a worldwide collection of pea germplasm. The variant tended to occur at higher frequencies in geographic regions with a cold climate. The fast allelic variant of H1-5 displayed a deletion resulting in the loss of a duplicated pentapeptide in the C-terminal domain.

The occurrence of a mutant dimerizable histone H5 in Japanese quail erythrocytes

An allelic variant of linker histone H5 has been found in the erythrocytes of Japanese quail (Coturnix japonica) descended from a small group of feral birds captured on the island of Hawaii. This variant spontaneously forms protein dimers in vitro in the absence of reducing agents. That this depends upon the introduction of a sulfhydryl group (presumably because of a cysteine substitution) is indicated by its reaction with 2-nitro-5-thiocyanobenzoate and by its fluorescence after reaction with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole. This is the first reported example of cysteine in a vertebrate linker histone and offers a specific reactive site for structural studies. A homozygous line for this form of H5 is being developed.