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1.
Mol Phylogenet Evol ; 178: 107666, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36384185

RESUMO

BACKGROUND AND AIMS: A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. METHODS: In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. KEY RESULTS: Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. CONCLUSIONS: Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.


Assuntos
Amomum , Zingiberaceae , Tamanho do Genoma , Filogenia , Amomum/genética , Zingiberaceae/genética , Genoma de Planta , DNA de Plantas/genética , DNA Ribossômico/genética , DNA de Cloroplastos
2.
Braz. j. biol ; 83: e245372, 2023. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1339409

RESUMO

Abstract Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one's (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.


Resumo A hibridização e a poliploidização são os fenômenos mais comuns observados em plantas, principalmente no gênero Nicotiana, levando à duplicação do genoma. Embora as mudanças genômicas associadas a esses eventos tenham sido estudadas em vários níveis, o tamanho do genoma e a variação do conteúdo de GC são menos compreendidos devido à ausência de dados genômicos suficientes. Neste estudo, a técnica de citometria de fluxo foi usada para descobrir o tamanho do genoma e o conteúdo de GC de 46 espécies de Nicotiana, e comparamos as mudanças genômicas associadas aos eventos de hibridização ao longo da escala de tempo evolutiva. O tamanho do genoma entre as espécies de Nicotiana variou entre 3,28 pg e 11,88 pg, enquanto os conteúdos de GC variaram entre 37,22% e 51,25%. As espécies tetraploides do gênero Nicotiana, incluindo as seções Polydiclae, Repandae, Nicotiana, Rustica e Sauveolentes, revelaram aumento e redução do tamanho do genoma quando comparados à soma dos genomas de suas espécies ancestrais. Os tamanhos do genoma de três híbridos homoploides foram encontrados perto de suas espécies ancestrais. A perda da grande sequência do genoma foi observada nas espécies evolutivas mais velhas (> 10 Myr) em comparação com as que evoluíram recentemente (< 0,2 Myr). Os teores de GC foram homogêneos com diferença média de 2,46% entre as espécies de Nicotiana. Conclui-se que a mudança no tamanho do genoma apareceu em ambas as direções, enquanto os conteúdos de GC foram encontrados mais homogêneos no gênero Nicotiana.


Assuntos
Tabaco/genética , Genoma de Planta/genética , Filogenia , Composição de Bases , Tamanho do Genoma
3.
Genet Res (Camb) ; 2022: 5417970, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36407084

RESUMO

Camellia nitidissima Chi (CNC), a species of golden Camellia, is well known as "the queen of camellias." It is an ornamental, medicinal, and edible plant grown in China. In this study, we conducted a genome survey sequencing analysis and simple sequence repeat (SSR) identification of CNC using the Illumina sequencing platform. The 21-mer analysis predicted its genome size to be 2,778.82 Mb, with heterozygosity and repetition rates of 1.42% and 65.27%, respectively. The CNC genome sequences were assembled into 9,399,197 scaffolds, covering ∼2,910 Mb and an N50 of 869 base pair. Its genomic characteristics were found to be similar to those of Camellia oleifera. In addition, 1,940,616 SSRs were identified from the genome data, including mono-(61.85%), di-(28.71%), tri-(6.51%), tetra-(1.85%), penta-(0.57%), and hexanucleotide motifs (0.51%). We believe these data will provide a useful foundation for the development of novel molecular markers for CNC as well as for further whole-genome sequencing of CNC.


Assuntos
Camellia , Theaceae , Camellia/genética , Theaceae/genética , Genoma de Planta/genética , Repetições de Microssatélites/genética , Tamanho do Genoma
4.
Sci Rep ; 12(1): 16635, 2022 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-36198853

RESUMO

Cryopreservation of rare plant materials is an important approach for preserving germplasms and is a good added concept to tissue banking. The preservation of embryogenic cell suspensions is even more valuable as the tissues facilitate in producing millions of embryos, plantlets and generates transgenics en masse. Catharanthus roseus is a medicinally important plant that produces a variety of anticancerous phytocompounds and needs conservation of alkaloid producing cell lines. In this study, embryogenic tissue banking has been attempted in C. roseus by the two-step cryopreservation method combining cryoprotection and dehydration. Prior to plunging into liquid nitrogen (LN), the tissues were exposed to osmotic-and cryoprotective agents. Two osmotic agents (sugar and sorbitol) and three cryoprotective compounds, polyethylene glycol (PEG), dimethyl sulfoxide (DMSO) and glycerol were used at varying concentrations to protect cells from freezing damages. Both sucrose and sorbitol increased callus biomass post-cryopreservation; the influence of sucrose was however, more prominent. Embryogenic tissue treated in medium with 0.4 M sucrose for 2 days followed by 5% PEG for 2 h showed maximum viability before (83%) and after (55%) cryopreservation, high regrowth percentage (77%) and produced an average 9 cell colonies per Petri dish. Additionally, dehydration (1-5 h) was tested to reduce water content for improving viability and regrowth of cryopreserved embryogenic cells. Among the various tested cryoprotective conditions, the highest (72%) viability was observed following the combination of treatments with 0.4 M sucrose (2 days),10% PEG (2 h) and dehydration (2 h). Maximum regrowth percentage (88%) and 12 colonies/petri dish was noted in combination of 0.4 M sucrose + 5% PEG. The cryopreserved calli differentiated into somatic embryos (52.78-54.33 globular embryos/callus mass) in NAA (0.5 mg/l) and BAP (0.5-1.0 mg/l) added media. Plantlets were successfully regenerated from cryopreserved tissue and the 2C DNA was estimated through flow cytometry. The genome size of cryopreserved regenerant was 1.51 pg/2C, which is similar to field-grown Catharanthus plants. Vinblastine and vincristine levels were nearly the same in mother plant's and frozen (cryopreserved) leaf tissue. The post cryopreservation embryogenesis protocol may be used for continuous production of plants for future applications.


Assuntos
Catharanthus , Crioprotetores , Criopreservação/métodos , Crioprotetores/farmacologia , Desidratação , Dimetil Sulfóxido/farmacologia , Desenvolvimento Embrionário , Tamanho do Genoma , Glicerol , Nitrogênio , Polietilenoglicóis , Sorbitol/farmacologia , Sacarose , Vimblastina/farmacologia , Vincristina/farmacologia , Água
5.
Genome Biol Evol ; 14(10)2022 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-36173740

RESUMO

The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.


Assuntos
Besouros , Genoma Mitocondrial , Animais , Besouros/genética , DNA Mitocondrial/genética , Evolução Molecular , Tamanho do Genoma , Filogenia
6.
J Genet ; 1012022.
Artigo em Inglês | MEDLINE | ID: mdl-36156510

RESUMO

Eucalyptus cloeziana is a valuable timber tree species for its high durability and excellent sawmilling qualities. However, there is lack of complete genomic information for this plant, which severely constrains its genetic improvement. This study aim to survey the genome of E. cloeziana and determine the large-scale sequencing scheme of this species. Next-generation sequencing based on Illumina Hi- Seq X Ten platform was used to survey the E. cloeziana genome and its SSR markers development. We estimated the genome size to be 491.91 Mb and the heterozygosity rate to be 1.23%, with repetitive sequences accounting for 40.74%. The clean reads of E. cloeziana were assembled into 995,093 scaffolds (556,992,952 bp) with a N50 value of 2297 bp. In the GO database, the 10,172 genes annotated were matched to 50 functional gene groups in three categories of cell component, biological function and molecular function, respectively. Through KEGG pathways analysis, 10,802 genes were successfully annotated and 133 metabolic pathways were detected with the most abundant metabolism-related genes. Meanwhile, a total of 58,832 simple-sequence repeat (SSR) loci were identified in the E. cloeziana genome, and among them, dinucleotide repeats were the most abundant class. AG/CT, AT/AT, AAG/CTT were the three most frequent primitive types. Of the 50 genomic SSR primer pairs randomly selected for screening test, 13 showed polymorphism (PIC = 0.625). Three to nine alleles per locus (mean = 6.23) were observed, with the observed and expected heterozygosity at 0.317-1.000 and 0.276-0.838 across all the 44 E. cloeziana germplasms, respectively. Here, we report the genome information of E. cloeziana, and the novel 13 genomic SSR markers that were developed can be used as powerful tools for evaluating genetic diversity and population structure, and thus contribute to molecular breeding studies of E. cloeziana and other eucalypts.


Assuntos
Eucalyptus , Eucalyptus/genética , Tamanho do Genoma , Genoma de Planta/genética , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites/genética , Análise de Sequência de DNA
7.
New Phytol ; 236(6): 2091-2102, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36110049

RESUMO

Grassland ecosystems cover c. 40% of global land area and contain c. 40% of soil organic carbon. Understanding the effects of adding nutrients to grasslands is essential because they provide much of our food, support diverse ecosystem services and harbor rich biodiversity. Using the meadow steppe (grassland) study site of Inner Mongolia, we manipulated seven key nutrients and a cocktail of micronutrients to examine their effects on grassland biomass productivity and diversity. The results, explained in structural equation models, link two previously disparate hypotheses in grassland ecology: (1) the light asymmetry competition hypothesis and (2) the genome size-nutrient interaction hypothesis. We show that aboveground net primary productivity increases predominantly from species with large genome sizes with the addition of nitrogen, and nitrogen plus phosphorus. This drives an asymmetric competition for light, causing a decline in species richness mainly in species with small genome sizes. This dynamic is likely to be caused by the nutrient demands of the nucleus and/or the scaling effects of nuclear size on cell size which impact water use efficiency. The model will help inform the best management approaches to reverse the rapid and unprecedented degradation of grasslands globally.


Assuntos
Ecossistema , Pradaria , Solo/química , Tamanho do Genoma , Carbono , Plantas/metabolismo , Nitrogênio/metabolismo , Nutrientes , Genoma de Planta
8.
Gene ; 846: 146866, 2022 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-36084895

RESUMO

Mesua ferrea is an important source of timber, oil and herbal medicines. In the present investigation, we assembled the whole chloroplast genome of M. ferrea of size 161.4 kb. The genome contained 86 protein-coding genes, 38 tRNAs, 8 rRNA genes and exhibited a characteristic quadripartite structural orientation, with two inverted repeats (27,614 bp) separated by an LSC (88,746 bp) region and an SSC (27,614 bp) (17,470 bp). Interestingly, no gene loss was identified in the M. ferrea genome, contrary to what has been observed in other Clusioid species. We compared the chloroplast genome of M. ferrea with the chloroplast genome of Bonnetia and Garcinia belonging to Bonnetiaceae and Clusiaceae families. Overall, the compared genomes possess a similar synteny of gene order except for a small inversion in Garcinia species. M. ferrea has the largest chloroplast genome size in Clusioid clade owing to the lengthening of the LSC, IR, and non-coding regions. Substantial differences were observed in population of simple sequence repeats (SSRs) and RNA editing sites among the studied genomes. A comparative assessment of chloroplast genomes revealed five highly divergence regions: rpl32, trnS-GCU_trnG-UCC, petN-psbM, psbZ_trnG-GCC and ccsA_ndhD among the analyzed sequences. Phylogenetic analyses and sequence homology search indicate that M. ferrea is closely related to the Garcinia species.


Assuntos
Genoma de Cloroplastos , Cloroplastos/genética , Tamanho do Genoma , Humanos , Repetições de Microssatélites/genética , Filogenia
9.
Int J Mol Sci ; 23(17)2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36077556

RESUMO

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.


Assuntos
Evolução Molecular , Retroelementos , Tamanho do Genoma , Genoma de Planta , Filogenia , Retroelementos/genética , Sequências Repetidas Terminais/genética
10.
Sci Rep ; 12(1): 14321, 2022 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-35995918

RESUMO

The study focuses on the propagation of a rare and endangered plant species (Pulsatilla patens) to re-introduce an extinct population from calamine area in Southern Poland. The plants were propagated from seeds, rhizome cuttings, or regenerated in vitro from shoot tips, hypocotyls with roots or cotyledons of seedlings on Murashige & Skoog (MS) medium supplemented with 0.25 or 0.50 mg L-1 BAP (Benzylaminopurine) via direct and indirect organogenesis or somatic embryogenesis (SE). The most efficient micropropagation method was with shoot tips as an explant on MS + 0.25 mg L-1 BAP where 97% of the explants produced multiple shoots, mass SE was observed after transfer on ½ MS with 2% saccharose; 267 (35%) shoots rooted on ½ MS + 2% saccharose were acclimatized to ex vitro conditions. Flow cytometry revealed genome size stability of propagated plantlets. Low genetic differentiation between micropropagated plantlets and initial material was indicated by ISSR (Inter Simple Sequence Repeat) markers. Totally, 132 vigorous plantlets obtained on various pathways were introduced to the field plots in 2020; 30.33% survived the winter, and several reached the generative stage and flowered in the spring 2021. In next season (March/April 2022) the number of introduced plants decreased to 25% while the number of flowering and fruiting shoots in different clumps increased in some plots. This is the first report of successful re-introduction of the endangered P. patens based on micropropagation, rhizome cuttings, and seed germination.


Assuntos
Anemone , Pulsatilla , Tamanho do Genoma , Repetições de Microssatélites , Pulsatilla/genética , Sementes/genética , Sacarose
11.
Genome ; 65(8): 459-468, 2022 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-35917258

RESUMO

Genome size (GS) or DNA nuclear content is considered a useful index for making inferences about evolutionary models and life history in animals, including taxonomic, biogeographical, and ecological scenarios. However, patterns of GS variation and their causes in crustaceans are still poorly understood. This study aimed to describe the GS of five Neotropical Synalpheus non-gambarelloides shrimps (S. apioceros, S. minus, S. brevicarpus, S. fritzmueller, and S. scaphoceris) and compare the C-values of all Caridea infraorder in terms of geography and phylogenetics. All animals were sampled in the coast of São Paulo State, Brazil, and GS was assessed by flow cytometry analysis (FCA). The C-values ranged from 7.89 pg in S. apioceros to 12.24 pg in S. scaphoceris. Caridean shrimps had higher GS than other Decapoda crustaceans. The results reveal a tendency of obtaining larger genomes in species with direct development in Synalpheus shrimps. In addition, a tendency of positive biogeographical (latitudinal) correlation with Caridea infraorder was also observed. This study provides remarkable and new protocol for FCA (using gating strategy for the analysis), which led to the discovery of new information regarding GS of caridean shrimps, especially for Neotropical Synalpheus, which represents the second-largest group in the Caridea infraorder.


Assuntos
Decápodes , Animais , Evolução Biológica , Brasil , Decápodes/genética , Tamanho do Genoma , Filogenia
12.
Genes (Basel) ; 13(8)2022 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-36011336

RESUMO

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.


Assuntos
Genoma de Cloroplastos , Tamanho do Genoma , Genoma de Cloroplastos/genética , Filogenia , Filogeografia , Poaceae/genética
13.
Planta ; 256(1): 18, 2022 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-35748952

RESUMO

MAIN CONCLUSION: Genome size of alpine plants is not related to their resistance against frost and heat. Genome size is a variable trait in angiosperms, and it was suggested that large genome size represents a constraint in stressful environments. We measured genome size and resistance to frost and heat in 89 species of plants from tropical and temperate alpine habitats. Genome size of the species, ranging from 0.49 pg to 25.8 pg across the entire dataset, was not related to either frost or heat resistance in either group of plants. Genome size does not predict resistance to extreme temperatures in alpine plants and is thus not likely to predict plant responses to climate changes.


Assuntos
Mudança Climática , Plantas , Tamanho do Genoma , Plantas/genética , Estações do Ano , Temperatura
15.
G3 (Bethesda) ; 12(8)2022 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-35758619

RESUMO

Brachymystax tsinlingensis Li, 1966 is an endangered freshwater fish with economic, ecological, and scientific values. Study of the genome of B. tsinlingensis might be particularly insightful given that this is the only Brachymystax species with genome. We present a high-quality chromosome-level genome assembly and protein-coding gene annotation for B. tsinlingensis with Illumina short reads, Nanopore long reads, Hi-C sequencing reads, and RNA-seq reads from 5 tissues/organs. The final chromosome-level genome size is 2,031,709,341 bp with 40 chromosomes. We found that the salmonids have a unique GC content and codon usage, have a slower evolutionary rate, and possess specific positively selected genes. We also confirmed the salmonids have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, and lost HoxAbß Hox cluster, highly expressed genes in muscle may partially explain the migratory habits of B. tsinlingensis. The high-quality B. tsinlingensis assembled genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.


Assuntos
Salmonidae , Animais , Composição de Bases , Cromossomos/genética , Tamanho do Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Filogenia , Salmonidae/genética
16.
Gigascience ; 112022 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-35764601

RESUMO

Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste, including landfill and incineration, usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, Trypoxylus dichotomus, can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of T. dichotomus, showing that the draft genome size of T. dichotomus is 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of T. dichotomus and the closely related scarabaeid species Onthophagus taurus occurred in the early Cretaceous (120 million years ago). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were 2 digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in T. dichotomus. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of T. dichotomus due to chromosomes 6 and 8 of T. dichotomus being intersected with chromosomes 2 and 10 of Tribolium castaneum, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of T. dichotomus, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in T. dichotomus.


Assuntos
Besouros , Animais , Cromossomos , Besouros/genética , Digestão , Tamanho do Genoma , Lignina , Filogenia , Transcriptoma
17.
Ann Bot ; 130(2): 189-197, 2022 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-35700050

RESUMO

BACKGROUND AND AIMS: Plant tissue nitrogen (N) and phosphorus (P) and genome traits, such as genome size and guanine-cytosine (GC) content, scale with growth or metabolic rates and are linked to plant ecological strategy spectra. Tissue NP stoichiometry and genome traits are reported to affect plant growth, metabolic rates or ecological strategies in contrasting ways, although the elemental costs for building and maintaining DNA are typically overlooked. METHODS: We formulated stoichiometry- and ecology-based predictions on the relationship between genome size and GC content to tissue N, P and N : P and tested them on a set of 130 herbaceous species from a temperate grassland using ordinary, phylogenetic and quantile regression. KEY RESULTS: Genome size was only negatively linked to plant N and N : P in species with very small genomes. We found no link between genome size and plant P. GC content was negatively linked to plant N and P but we found these significant links consistently in both GC-rich and GC-poor species. Finally, GC content correlated positively with plant N : P but only in species with GC-rich genomes. CONCLUSIONS: Our results provide stronger support for the ecology-based predictions than the stoichiometry-based predictions, and for the links between GC content and plant N and P stoichiometry than for genome size. We argue that the theories of plant metabolic rates and ecological strategies (resource-acquisitive vs. conservative or ruderal vs. stress-tolerator spectra) better explain interspecific genome-NP stoichiometry relationships at the tissue level (although relatively weakly) than the stoichiometric theory based on the elemental costs for building and maintaining DNA.


Assuntos
Nitrogênio , Fósforo , Composição de Bases , Citosina/metabolismo , Tamanho do Genoma , Pradaria , Guanina/metabolismo , Nitrogênio/metabolismo , Fósforo/metabolismo , Filogenia , Plantas/metabolismo
18.
Evolution ; 76(7): 1453-1468, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35657770

RESUMO

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.


Assuntos
Evolução Biológica , Urodelos , Animais , Tamanho Corporal , Tamanho Celular , Tamanho do Genoma , Urodelos/anatomia & histologia
19.
New Phytol ; 236(2): 433-446, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35717562

RESUMO

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.


Assuntos
Arecaceae , Retroelementos , Arecaceae/genética , Evolução Molecular , Tamanho do Genoma , Genoma de Planta , Filogenia , Análise de Sequência de DNA
20.
Can J Microbiol ; 68(8): 561-568, 2022 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-35623096

RESUMO

Urnula craterium (Schwein.) Fr. (1851) has been reported from North America, Europe, and Asia, and can be a pathogen on various hardwood species. In this study, we investigated the mitochondrial genome of U. craterium. The biology and taxonomy of this fungus is poorly studied and there are no mitogenomes currently available for any member of the Sarcosomataceae (Order Pezizales). The complete mitogenome of U. craterium comprises 43 967 bps and encodes 14 protein-coding genes, a complete set of tRNAs and rRNA genes. A novel feature of the mitogenome is the presence of a single subunit DNA polymerase-coding region that is typically associated with linear invertron-type plasmids. The mitogenome may offer insights into the evolution of mitogenomes among members of the Pezizales with regards to gene content and order, mobile elements, and genome sizes.


Assuntos
Ascomicetos , Genoma Mitocondrial , Ascomicetos/genética , Tamanho do Genoma , Fases de Leitura Aberta , Filogenia
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