Amaranthaceae Species Research Articles

Amaranthaceae Pollen Trends in the Air

Understanding the trends of airborne pollen allergens is of great importance given the high prevalence and socioeconomic impact of pollen-related allergic diseases globally. To study the morphological features of Amaranthaceae pollen, assess its contribution to the aerobiological situation in the city of Karakol and identify periods of increased concentration in order to improve the diagnosis and prevention of pollinosis symptoms in patients. Aerobiological sampling using a Lanzoni pollen trap was carried out from April to October over a three-year period (2015–2017) in Karakol city. Pollen identification and differential counting were performed according to current standard methodology and specially developed guides and atlases. Pollen characteristics of 4 Amaranthaceae species were visualized using scanning electron microscopy (Hitachi) to provide a detailed understanding of the surface structure and ornamentation of pollen grains. The decadal curve of Amaranthaceae pollen concentration in Karakol is unimodal, with often overlapping quantitative characteristics: 6615 (2nd decade of August 2015), 1326 (1st decade of 2016), 444 pollen grains / m3 (1st decade of 2017). At the same time, strong interannual variability of atmospheric pollen levels was observed, depending both on the pollen production of the plants themselves and on meteorological parameters, especially temperature and precipitation, changes in the traditional farming system. The response of summer-flowering Amaranthaceae weeds to climate change was demonstrated, which consists in a decrease in the annual pollen index, which corresponds to the global trend. Peak concentrations of Amaranthaceae pollen many times exceeded clinical threshold values in the air. On the surface of the Bassia scopariapollen exine, the ultrastructure study revealed the smallest (1.5-2.0 μm) granules of sporopollenin or orbicules (Ubisch bodies), which play a role in the spread of allergens. The obtained data are important in terms of increasing public awareness of the dominant pollen of the Amaranthaceae family, optimizing diagnostics, treatment and prevention of pollinosis.

Dopamine-derived pigments in nature: identification of decarboxybetalains in Amaranthaceae species.

A unique family of decarboxylated betalains derived from dopamine has recently been discovered. Due to the lack of chemical standards, the existence and distribution of decarboxylated betalains in nature remain unknown. Traditional betalains contain L-dihydroxyphenylalanine as the starting point of the biosynthetic pathway and betalamic acid as a structural and functional unit, while the recently discovered betalains rely on dopamine. Here, 30 dopamine-derived betalains were biotechnologically produced, purified, and characterized, creating an unprecedented library to explore their properties and presence in nature. The maximum absorbance wavelengths for the pigments ranged between 461 and 485 nm. HPLC analysis showed retention times between 0.6 and 2.2 min higher than traditional betalains due to their higher hydrophobicity. The presence of decarboxybetalains in nature was screened using HPLC-ESI-Q-TOF mass spectrometry in various species of the Amaranthaceae family: beetroot (Beta vulgaris subsp. vulgaris), Swiss chard (B. vulgaris var. cicla), celosia (Celosia argentea var. plumosa), and quinoa (Chenopodium quinoa). The latter species had the highest content of decarboxybetalains (28 compounds in its POEQ-143 variety). Twenty-nine pigments were found distributed among the different analyzed plant sources. The abundance of decarboxybetalains demonstrated in this work highlights these pigments as an important family of phytochemicals in the order Caryophyllales.

Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides.

Alternanthera sessilis is considered the closest relative to the invasive weed Alternanthera philoxeroides in China, making it an important native species for studying the invasive mechanisms and adaptations of A. philoxeroides. Chloroplasts play a crucial role in a plant's environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of A. sessilis has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis chloroplast genome. Moreover, two genes, ccsA and accD, were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between A. philoxeroides and A. sessilis to be approximately 3.5186-8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the Alternanthera genus.

Complete Chloroplast Genome of Krascheninnikovia ewersmanniana: Comparative and Phylogenetic Analysis.

Krascheninnikovia ewersmanniana is a dominant desert shrub in Xinjiang, China, with high economic and ecological value. However, molecular systematics research on K. ewersmanniana is lacking. To resolve the genetic composition of K. ewersmanniana within Amaranthaceae and its systematic relationship with related genera, we used a second-generation Illumina sequencing system to detect the chloroplast genome of K. ewersmanniana and analyze its assembly, annotation, and phylogenetics. Total length of the chloroplast genome of K. ewersmanniana reached 152,287 bp, with 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Codon usage analysis showed the majority of codons ending with base A/U. Mononucleotide repeats were the most common (85.42%) of the four identified simple sequence repeats. A comparison with chloroplast genomes of six other Amaranthaceae species indicated contraction and expansion of the inverted repeat boundary region in K. ewersmanniana, with some genes (rps19, ndhF, ycf1) differing in length and distribution. Among the seven species, the variation in non-coding regions was greater. Phylogenetic analysis revealed Krascheninnikovia ceratoides, Dysphania ambrosioides, Dysphania pumilio, and Dysphania botrys to have a close monophyletic relationship. By sequencing the K. ewersmanniana chloroplast genome, this research resolves the relatedness among 35 Amaranthaceae species, providing molecular insights for germplasm utilization, and theoretical support for studying evolutionary relationships.

Genome-wide identification and salt stress-expression analysis of the dehydrin gene family in Chenopodium quinoa

Dehydrins (DHNs) are essential proteins in the embryonic development and abiotic stress responses of plants. Due to their remarkable ability to confer tolerance to plants in conditions of drought, salinity and extreme temperatures, DHNs have garnered considerable interest. Quinoa (Chenopodium quinoa Willd.), a facultative halophyte plant, can thrive in a wide range of agroecosystems, making it a promising candidate for stress tolerance studies. In this study, we identified eleven DHN genes in the quinoa genome belonging to Y-, F- and H-orthologous groups found in angiosperms. Notably, the H-DHNs lack the K-segment, a feature observed in all Amaranthaceae species, but not in other angiosperms. We identified four DHN structural subgroups: FSKn, YnSKn, SKn-DHNs and the atypical HS-DHN. Phylogenetic analysis indicated that each structural subgroup, except for SK2-DHN, presents two paralogous genes, in accordance with the allotetraploid character of C. quinoa. Quantitative real-time PCR expression analysis revealed that DHN1s (FSK2) and DHN3s (Y2SK2) were expressed in all tissues, while DHN2s (FSK3) were predominant in roots and DHN4s (Y4SK2 and SK2) were predominant in flowers. Salt-response gene expression analysis in seedlings showed that CqDHN4s increase their expression in response to salt stress in all varieties studied, while CqDHN1s reduce their expression in a more salt stress-tolerant variety, suggesting a possible adaptive advantage. In silico analysis of the promoters of CqDHN1s and CqDHN4s supports the involvement of these DHNs in responding to abiotic stress.

Aceria spp. (Acari: Eriophyidae) associated with Amaranthaceae around the world with description of two new species</p >

During field surveys of eriophyoid mites in Razavi and North Khorasan provinces (Iran) in summer 2023, two new Aceria spp. (Acari: Eriophyoidea: Eriophyidae) on Amaranthaceae plants were discovered, illustrated and described: Aceria sodae sp. nov. on Soda rosmarinus (Bunge ex Boiss.) Akhani and Aceria esfarayeniensis sp. nov. on Salsola arbusculiformis Drobow. Furthermore, a list of Aceria spp. on Amaranthaceae species around the world, their type host plants and their relationship to hosts are provided.

Genetic Polymorphism in the Amaranthaceae Species in the Context of Stress Tolerance.

The adaptive potential and biochemical properties of the Amaranthaceae species make them promising for introduction into agriculture and markets, particularly in arid conditions. Molecular genetic polymorphism analysis is the most powerful tool for studying plant resources; therefore, the current study aimed to investigate the polymorphisms of allelic variations in the ARF and SOD gene families, as well as the genetic diversity of six Amaranthaceae species, using retrotransposon-based fingerprinting with the multi-locus EPIC-PCR profiling approach. Additionally, the iPBS PCR amplification was employed for genome profiling, revealing variations in genetic diversity among the studied Amaranthaceae samples. The observed genetic diversity in Amaranthaceae species contributes to their enhanced tolerance to adverse environmental conditions. The knowledge about the genetic diversity of genes crucial in plant development and stress resistance can be useful for the genetic improvement of cultivated Amaranthaceae species.

Unveiling the intricacies of Amaranthaceous pollen diversity: Advancing ultra sculpture analysis through LM and SEM.

Microscopic techniques can be applied to solve taxonomic problems in the field of plant systematic and are extremely versatile in nature. This study was focused on the new approaches to visualizing the imaging, tool to cover the micro-structural techniques applied to the pollen study of Amaranthaceae floral biology. In this detailed study, we used light microscopy and scanning electron microscopy to examine the shape and changes in pollen of 16 types of Amaranthaceae plants from the salty arid zone of Riyadh Saudi Arabia. We observed subtle variations among the studied species through meticulous examination of morpho-palynological features such as symmetry, size, shape, pore ornamentation, and exine characteristics. The pollen grains were round and had rough or prickly outer coverings. They had different numbers of tiny pores; some were slightly sunken. These findings were utilized to develop a pollen taxonomy key, facilitating accurate identification and classification of Amaranthaceous species. Our results shed light on the taxonomic significance of pollen morphology for species differentiation within the Amaranthaceae family. Furthermore, this study provides valuable insights into the influence of geographical and ecological factors on pollen diversity and evolution. This study of pollen imaging visualization of Amaranthaceous species contributes to the opportunity for taxonomic evaluation and fill knowledge gaps in studies of Amaranthaceous flora identification using classical microscopic taxonomic tools for their accurate identification. RESEARCH HIGHLIGHTS: The pollen characters of selected Amaranthaceae species were visualized using scanning electron microscopy to observe sculptural wall pattern. The comprehensive Amaranthaceous pollen examination approach allowed us to accurately identify their micromorphology. This high-resolution imaging technique provided detailed insights into the surface structures and ornamentation of the pollen grains.

Native plant diversity for ecological reclamation in Moroccan open-pit phosphate mines.

Mining activities have significant impacts on the environment, particularly in terms of the destruction of natural habitats andbiodiversity loss. With the increasing awareness of the importance of ecological restoration and conservation, there is a growing need to study and understand the flora that thrives in mining sites in order to facilitate successful reclamation efforts. This study aimed to investigate the floristic composition and plant diversity of four phosphate mine sites (PMSs) in Morocco, namely Bou Craa mine (BCM), Ben Guerir mine (BGM), Youssoufia mine (YSM), and Khouribga mine (KHM). The study found a total of 215 vascular plant species from 166 genera and 49 taxonomic families across the four sites. BGM was the most diverse site with 120 plant species, followed by KHM with 75, YSM with 57, and BCM with 54. Compositae family species were the most common at BGM and KHM, while Amaranthaceae species were dominant at BCM, and Poaceae and Compositae at YSM. Therophytes (annual species) were the most common functional group (45.0%), followed by chamaephytes (19.6%) and hemicryptophytes (15.9%). Atriplexnummularia and Chenopodiumalbum were the most common species found at all four sites, while Atriplexsemibaccata, Bassiamuricata, Haloxylonscoparium, and 12 other species were common at three sites. However, 156 plant species were found at only one site. The findings of this study highlight the significant abundance of plant species in Moroccan PMSs and provide a basis for successful ecological engineering rehabilitation plans. The study emphasizes the importance of studying the indigenous plant species that naturally populate these marginal lands to ensure successful reclamation efforts.

Non-structural carbohydrates stored in belowground organs point to the diversity in Amaranthaceae

Amaranthaceae is a cosmopolitan and diverse family, with characteristics that enable plants to occupy habitats with harsh environmental conditions. The Brazilian Cerrado has numerous features that impose challenges to plant survival, such as seasonal drought and fires. Nearly one hundred species of Amaranthaceae occur in the Cerrado and many of them have thickened belowground systems that store non-structural carbohydrates. In this study, we analyze patterns in the adaptive strategies of Amaranthaceae species that occur in the Cerrado, by assessing the types of carbohydrates stored in the belowground systems and biomass allocation in light of photosynthetic characteristics reported in the literature. We analyzed species of Amaranthus (C4), Alternanthera (C3-C4), Froelichia (C4), Gomphrena (C4), and Pfaffia (C3). All the analyzed species had non-structural carbohydrate content higher than 20% of the dry mass. Sucrose was the main non-structural carbohydrate found in the belowground organs of Alternanthera tenella and Amaranthus viridis. Starch was detected only in Amaranthus viridis. All other species accumulate fructans; Pfaffia spp. have inulin-type fructans while Gomphrena and Froelichia have levan-type fructans. Two morphophysiological syndromes are characterized by the lowest or highest investment in belowground system mass and storage of fructans, being interpreted as generalist or specialist adaptive strategies. These two characteristics of such syndromes, together with the photosynthetic metabolisms are traits that reflect the diversity of the Amaranthaceae and their ability to occupy several habitats, including those marked by harsh conditions, such as the Cerrado.

Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa

BackgroundChenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa.ResultsWe identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.ConclusionsThe present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa’s resistance to salt stress.

Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

BackgroundChloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family.ResultsMethodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae.ConclusionsThis study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.

Isolation and characterization of Salt Overly Sensitive family genes in spinach

The Salt Overly Sensitive (SOS) pathway regulates intracellular sodium ion homeostasis as a salt-stress response in plants. This pathway involves three main genes designated as SOS1, SOS2 and SOS3, which are members of the Na+ /H+ exchanger (NHX), CBL-interacting protein kinase (CIPK) and Calcineurin B-like (CBL) gene families, respectively. To identify and characterize SOS genes in spinach (Spinacia oleracea), a species of the Amaranthaceae family, we conducted genome-wide identification and phylogenetic analyses of NHX, CIPK and CBL genes from four Amaranthaceae species, Arabidopsis and rice. Most Amaranthaceae genes exhibited orthologous relationships with Arabidopsis and/or rice, except a clade of Vac-type Amaranthaceae NHX genes. Phylogenetic analyses also revealed gene gain/loss events in Amaranthaceae species and the intron-less to intron-rich evolution of CIPK genes. A bacterial protein-rooted CIPK tree allowed naming most of the phylogenetic clades based on their evolutionary history. Single S. oleracea (So) SOS1, SOS2 and SOS3 proteins were identified. Direct protein-protein interaction was observed between SoSOS2 and SoSOS3 but not between SoSOS2 and SoSOS1 based on yeast two-hybrid assay. This may suggest distinct modes of action of spinach SOS proteins compared to Arabidopsis SOS proteins. Unlike SoSOS1 and SoSOS2, which were expressed at similar or higher levels in leaves than roots, SoSOS3 expression was significantly higher in roots than leaves, suggesting its greater importance in roots. The expression of SoSOS3 was upregulated in both roots and leaves under salinity compared to the control; however, SoSOS1 was only upregulated in roots. Thus, this study demonstrated the conservation of SOS pathway genes in spinach and also highlighted the complexity of SOS signaling in Amaranthaceae species.

Chromosome number and genome size in Atriplex mollis from southern Tunisia and Atriplex lanfrancoi from Malta (Amaranthaceae)

In this work, we investigated the chromosome number and genome size of two Mediterranean Amaranthaceae species, namely Atriplex mollis from southern Tunisia and A. lanfrancoi (formerly Cremnophyton lanfrancoi) from Malta. The two species were found to be diploid (2n = 18) for all examined populations. This result is different from that previously reported for Cremnophyton lanfrancoi Brullo and Pavone (2n = 20). Genome size showed that both species have a close mean amount with 2C = 3.41 and 3.51 pg, respectively. Two groups were distinguished with regard to genome size (P < 0.01). It should, however, be noted that the majority of populations, with the exception of those from Djerba and Chbika, may be intermediate between the two basic groups. Moreover, the difference does not appear to depend on geographical distribution and environmental aspects. It would rather depend on chromosome rearrangements. The morphological similarities, the monophyly of Atriplex including A. lanfrancoi, previously ranked in genus Cremnophyton, sharing the same chromosome number and the same genome size, support the placement of Cremnophyton within the genus Atriplex.

Genome‐wide microsatellite characterisation and marker development in Chenopodium quinoa

AbstractMicrosatellites, as the tracts of repetitive DNA, are an essential constituent of the plant genome that holds important evolutionary significance, and have been extensively used to develop molecular makers for genetic analysis. To understand the microsatellite dynamics of quinoa genome and its relatives, in this study we performed a genome‐wide analysis of microsatellites in five Amaranthaceae species using available genome sequences. The results demonstrated that the microsatellites of the five Amaranthaceae species were characterised by relatively high proportions of mono‐, di‐ and trinucleotide repeats with A/T rich motifs, implying conservative organisation and composition of microsatellites in this family. Furthermore, a significant negative correlation between microsatellite frequencies and GC contents (r = −.87) were observed. In total, 533,961 (89.57%) and 542,601 (89.86%) microsatellite loci could be used to develop simple sequence repeat (SSR) molecular markers, of which 7,178 were found to be polymorphic between the two sequenced quinoa cultivars, QQ74 and Real Blanca, through in silico PCR analysis. Finally, 15 SSR markers were randomly selected to validate their polymorphism across 12 quinoa accessions by wet‐lab PCR amplification. The newly developed genome‐wide SSR markers provide a useful resource for population genetics, gene mapping and molecular breeding studies in quinoa and beyond.

Studies on underutilized weeds of family Amaranthaceae used as edibles by the Munda tribe of Jharkhand, India.

Amaranthaceae, a common family of flowering plants distributed worldwide, also shows its presence in Jharkhand. Jharkhand have some of the species which are wild growing and are considered as weeds. The people of Munda tribe have a rich traditional knowledge of utilizing these weeds as edibles and for medicines. This paper deals with the study and documentation traditional knowledge of Mundas, which resulted in documentation of seven wild growing underutilized Amaranthaceae species. This type of documentation work is very important in the present century where the natural resources and their related knowledge are depleting due to unawareness about their importance and utilities.

Synteny-based mapping of causal point mutations relevant to sand rice (Agriophyllum squarrosum) trichomeless1 mutant by RNA-sequencing

Sand rice (Agriophyllum squarrosum), a diploid Amaranthaceae species within the order Caryophyllalles, has potential as a crop in response to concerns about ongoing climate change and future food security. Modifying the weedy traits, such as dense trichomes, is important for the domestication of sand rice. In this study, an ethyl methanesulfonate (EMS) induced Agriophyllum squarrosum trichomeless mutant (astcl1) was isolated and genetic analysis revealed that this mutant was controlled by a single recessive locus. RNA sequencing was employed to analyze sequence variations between the mutant and wild-type individuals based on allele frequencies. Synteny-based mapping against two closely related and sequenced species finally delimited the causal mutations into an approximately 18.97 mega base pair (Mb) interval on the top portion of the chromosome 6 (Bv6) of sugar beet (Beta vulgaris) and two intervals (5.56 and 2.69 Mb) on the chromosomes 14 (CqA14) and 6 (CqB06) of quinoa (Chenopodium quinoa). These two quinoa intervals were located in the orthologous chromosomal regions against sugar beet Bv6. Differential expression analysis revealed that the astcl1 mutation only affects the expression of a small subset of genes. Most significantly, 17 lipid transport and metabolism related genes, such as GDSL esterases and very-long-chain 3-oxoacyl-CoA reductase 1, and two R2R3 MYB genes, MYB39 and RAX3, were down-regulated in astcl1 mutants. These results imply that the Astcl1 protein coordinately regulates trichome initiation and cuticle biosynthesis in sand rice.

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

BackgroundAmaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species.ResultsUtilizing single-molecule, real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C) to close assembly gaps and scaffold contigs, respectively, we improved our previously reported Illumina-based assembly to produce a chromosome-scale assembly with a scaffold N50 of 24.4 Mb. The 16 largest scaffolds contain 98% of the assembly and likely represent the haploid chromosomes (n = 16). To demonstrate the accuracy and utility of this approach, we produced physical and genetic maps and identified candidate genes for the betalain pigmentation pathway. The chromosome-scale assembly facilitated a genome-wide syntenic comparison of amaranth with other Amaranthaceae species, revealing chromosome loss and fusion events in amaranth that explain the reduction from the ancestral haploid chromosome number (n = 18) for a tetraploid member of the Amaranthaceae.ConclusionsThe assembly method reported here minimizes cost by relying primarily on short-read technology and is one of the first reported uses of in vivo Hi-C for assembly of a plant genome. Our analyses implicate chromosome loss and fusion as major evolutionary events in the 2n = 32 amaranths and clearly establish the homoeologous relationship among most of the subgenome chromosomes, which will facilitate future investigations of intragenomic changes that occurred post polyploidization.

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses.

Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.