Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms.

Chloroplast genomes (plastomes) have long been considered structurally conserved, but recent sequencing efforts have uncovered pervasive rearrangements that challenge this assumption. This review catalogues the main types of plastome modifications: large and small inversions; insertions and deletions (indels); gene and intron losses; horizontal gene transfers; shifts in inverted repeat boundaries; and gene duplications. It then explains the molecular processes that generate these changes, from repeat-mediated recombination and slipped-strand mispairing to rare foreign-DNA integration events.

Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae).

Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino acid production, and stress responses. The genus Passiflora, known for its species diversity and dynamic chloroplast (cp) genome evolution, serves as an excellent model for studying structural variations. This study investigates evolutionary relationships within Passiflora by sequencing 11 new chloroplast genomes, assessing selective pressures on cp genes, and comparing plastid and nuclear phylogenies.

Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.

Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka.

Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns.

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C.

Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes.

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity.

Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.

One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N.

Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae).

Background And Aims: The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia.

Methods: We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework.

A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis.

The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g.

Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome.

While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known.

A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes.

Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group.

Improving yield and fruit quality traits in sweet passion fruit: Evidence for genotype by environment interaction and selection of promising genotypes.

Breeding for yield and fruit quality traits in passion fruits is complex due to the polygenic nature of these traits and the existence of genetic correlations among them. Therefore, studies focused on crop management practices and breeding using modern quantitative genetic approaches are still needed, especially for Passiflora alata, an understudied crop, popularly known as the sweet passion fruit. It is highly appreciated for its typical aroma and flavor characteristics.

Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis.

A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species.

Corrigendum: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations.

[This corrects the article DOI: 10.3389/fgene.2018.

A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species.

Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis.

Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations.

Traditional sugarcane cultivars () proved highly susceptible to diseases, and this led breeders to progress to interspecific crosses resulting in disease resistance. A backcrossing program to was then required to boost sucrose content. Clonal selection across generations and incorporation of other germplasm into cultivated backgrounds established the (narrow) genetic base of modern cultivars ( spp.

The Chloroplast Genome of (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.

The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus . In Brazil, the yellow passion fruit () is of considerable economic importance, both for juice production and consumption as fresh fruit.