Comparative Population Studies Research Articles

Complete Circularized Genome Resources for Xylella fastidiosa subsp. sandyi Strains CO33 and CFBP8478

Xylella fastidiosa ( Xf) is a vascular phytopathogenic bacterium native to the Americas, known for causing severe diseases and significant economic losses in important crops. In Europe, Xf is considered a quarantine pathogen. Since its first detection in 2013 in Italy, mandatory surveys to search for Xf across Europe have revealed the presence of three Xf subspecies ( fastidiosa, multiplex, and pauca) in different outbreaks occurring in France, Spain, and Portugal. Xf subspecies sandyi and morus have not been associated with epidemic outbreaks in Europe; however, subspecies sandyi has been detected in intercepted plants imported from Costa Rica and Honduras. By combining data from the Oxford Nanopore Technologies and Illumina sequencing platforms, we obtained complete genomes for Xf strains CO33 and CFBP8478. Both strains belong to the subspecies sandyi and were isolated from coffee plants intercepted in Europe that were imported from Costa Rica. These two genome resources increase the scarce number of Xf genomes available belonging to the subspecies sandyi, which is crucial for comparative genomic analysis and population studies of this important plant-pathogenic bacterium. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea.

Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level. Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina. Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers. The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754. Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.

The Past, Present and Future of CPoS

In this editorial note, we reflect on the trajectory of Comparative Population Studies (CPoS) over the last decades, highlight major milestones along the road, and sketch our hopes and ideas for its future development. In 1975, the predecessor journal of CPoS named ZfB was established as the scientific journal of the newly founded German Federal Institute for Population Research (BiB). As the Institute grew its international collaborations and the journal transitioned from German to English language, ZfB became CPoS. Today, we are pleased that the journal has grown in statue and attracts high-quality submissions from scholars around the globe. Looking ahead, we envision CPoS as a unique open-access journal in the field of population studies where innovation, scientific rigor and attention to quality work hand-in-hand to advance population studies and respond to societal challenges.

Width/length–weight relationships and condition factor of seven decapod crustaceans in a Brazilian tropical estuary

The analysis of body relationships and condition factors are useful tools in studies of marine populations, and they have been widely used in fishery research and management. In this study, width–weight (WWR) and length–weight (LWR) relationships and Fulton’s condition factors were analyzed for six commercially important decapod crustacean species from the Paraguaçu River estuary (Todos os Santos Bay), eastern Brazil, namely Callinectes danae, C. exasperatus, C. marginatus, C. ornatus, Goniopsis cruentata and Ucides cordatus, and one non-indigenous species, Charybdis helleri. In total 5,704 individuals were measured and weighed during five years (2012–2017). The three allometric growth types for the crustacean species were observed, being most frequently the negative allometric growth. The analysis of covariance (ANCOVA) revealed significant differences between the sexes and climatic seasons in WWR/LWRs for the four species of the genus Callinectes, C. helleri, G. cruentata and U. cordatus, except for females and males of C. danae in WWR. The means for condition factor were generally higher for females than for males during the dry period, and in general, indicating good conditions for crustacean species. This study provided morpho-biometric parameters information will contribute stock management of traditional artisanal fisheries, and enable future comparative studies of populations of the same species.

Do Suburban Populations of Lizards Behave Differently from Forest Ones? An Analysis of Perch Height, Time Budget, and Display Rate in the Cuban Endemic Anolis homolechis

Urbanization transforms natural ecosystems into novel habitats, which can result in negative consequences for biodiversity. Therefore, it is important to understand the mechanisms of maintenance of native species in urbanized environments, including behavior—which can act as a fast response to rapid environmental changes. We compared some behavioral traits between two suburban and two forest populations of Anolis homolechis. Direct observations of 779 individuals revealed that perch height was positively influenced by body size, but not by sex. Suburban individuals perched higher than forest ones, and even more so in the afternoon compared to the morning; a behavior that was not observed in forests populations. These differences might be due to a change from foraging activities in the morning to vigilance, display, and/or thermoregulation in the afternoon, promoted by suburban habitat conditions (e.g., higher predator abundance, open habitat structure, and urban heat). Video recordings of 81 focal individuals showed that males were more active than females (i.e., spending less time in stationary behavior and having a higher display rate), with no significant effect of habitat type. As some of our results diverge from previous studies on invasive anoles, we recommend extending comparative studies of urban and non-urban populations to other native Anolis.

FRAILTY AND SOCIOECONOMIC STATUS IN BRAZIL, CHINA, AND INDIA

Abstract Frailty, the vulnerability to poor health outcomes following physiologic stress, acts as a measure of physiological age that can be used to compare the health of older populations. Using a frailty index validated in multiple countries, we looked at the relationship between four measures of socio-economic status (SES) and frailty in Brazil, China, and India. For SES measures, we considered within-country income and wealth deciles, education level, and rural residence. Analysis used beta regression, first within each country, then with combined data with country fixed effects and country-by-SES interactions. We found evidence of strong, statistically significant negative associations between education level and frailty in all three countries. Associations between frailty and income or wealth decile or rural residence were small and inconsistently statistically significant. This demonstrates the key role of education for healthy aging and the value of harmonized frailty measures for comparative studies of older populations.

Genetic diversity and gene expression diversity shape the adaptive pattern of the aquatic plant Batrachium bungei along an altitudinal gradient on the Qinghai-Tibet plateau.

It is an intriguing issue of evolutionary biology how genetic diversity and gene expression diversity shape the adaptive patterns. Comparative transcriptomic studies of wild populations in extreme environments provide critical insights into the relative contribution of genetic and expressive components. In this study, we analyzed the genetic diversity and gene expression diversity of 20 populations of the aquatic plant Batrachium bungei along elevations ranging from 2690 to 4896m on the Qinghai-Tibet plateau (QTP). Based on single nucleotide polymorphisms (SNPs) and gene expression data from 100 individuals of B. bungei, we found that variation in genetic sequence was more sensitive to detect weak differentiation than gene expression. Using 292,613 high-quality SNPs, we documented a significant phylogeographical structure, a low within-population genetic diversity, and a high inter-population genetic differentiation in B. bungei populations. Analysis of relationship between geographic distance, genetic distance, and gene expression similarity showed that geographic isolation shaped gene flow patterns but not gene expression patterns. We observed a negative relationship between genetic diversity and gene expression diversity within and among B. bungei populations, and we demonstrated that as environmental conditions worsen with increasing altitude, genetic diversity played an increased role in maintaining the stability of populations, while the corresponding role of gene expression diversity decreased. These results suggested that genetic diversity and gene expression diversity might act as a complementary mechanism contributing to the long-term survival of B. bungei in extreme environments.

Comparison of Molecular Characteristics Between Methicillin-Resistant and -Susceptible Staphylococcus aureus Clinical Isolates by Whole-Genome Sequencing.

IntroductionThe transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) are great public health concern worldwide. To better understand S. aureus evolution and dissemination, we compared the molecular features of MSSA and MRSA isolates.MethodsIn this study, 74 MSSA and 102 MRSA non-duplicate isolates were recovered from clinical samples between 2016 and 2020. Molecular epidemiology, antimicrobial resistance determinants, and virulence gene profiles were carried out by whole-genome sequencing (WGS).ResultsTwenty distinct sequence types were identified in MRSA isolates, with the most common being ST59, ST630, and ST338. The major genotypes of MSSA were ST188 and ST7. The toxin genes clfA, sek, and seq were significantly associated with MRSA, while splA/B, clfB, map, sdrC/D, and sem-sen-seo-seu were detected more frequently in MSSA isolates than MRSA (P < 0.05). The tst positive isolates were more commonly identified in CC1 and CC72, whereas lukE/D was mainly found in the CC7, CC15, CC88, and completely absent in CC59 clones.ConclusionOur results compared the genetic diversity between MRSA and MSSA strains, suggesting efforts to fight infections caused by MSSA need to be intensified due to MSSA isolates carrying wide range of virulence factors. Comparative epidemiological studies of large populations of MSSA and MRSA will be necessary in the future to understand how MSSA and MRSA populations may co-evolve and interact in the future.

PSATdb: a database of mitochondrial common, polymorphic, and unique microsatellites.

Microsatellites, also termed as simple sequence repeats, are repetitive tracts in a DNA sequence, typically consisting of one to six nucleotides. These repeats are found in all genomes and play key roles in phylogeny and species identification. Microsatellites are highly polymorphic, and their length may differ from species to species. There are several online resources dedicated to mitochondria; however, comprehensive information is not available about the length variation of mitochondrial microsatellites. Therefore, to explore it between species among a genus, we have developed a database named pSATdb (polymorphic microSATellites database; https://lms.snu.edu.in/pSATdb/). pSATdb contains 28,710 perfect microsatellites identified across 5,976 mitochondrial genome (mt-genome) sequences from 1,576 genera which includes 1,535 (5,846 mt-genome) and 41 (130 mt-genome) genera of Metazoa and Viridiplantae, respectively. pSATdb is the only database which provides genus-wise information about the length variation of mitochondrial microsatellites. Because of the emerging role of microsatellites in genomics studies, the identified common, polymorphic, and unique microsatellites stored in pSATdb will be effectively useful in various studies including genetic diversity, mapping, marker-assisted selection, and comparative population studies.

Spatiotemporal variation in the adult sex ratio, male aggregation, and movement of two tropical cloud forest dung beetles.

While theory suggests that at conception the sex ratio should be balanced (1:1), this can be variable across space and time in wild populations. Currently, studies of the environmental factors that regulate adult sex ratio (ASR) in species with different life history traits are scarce. Using capture-recapture over a year, we analyzed the influence of habitat type (forest and nonforest) and season (rainy and dry) on variation in ASR, male aggregation and the trajectory movement of 2 dung beetle species with different life history traits: Deltochilum mexicanum (a hornless roller species) and Dichotomius satanas (a tunneler species with horns on its head and thorax). We found opposite tendencies. The D. mexicanum population tends to be female-biased, but the population of D. satanas tends to be predominantly male, and observed values were not related to habitat type or season. However, the 95% confidence intervals estimated were highly variable between seasons depending on habitat. On examining the monthly variation in ASR for both habitats, we found that it depends on the species. In addition, male aggregation differed between species depending on habitat type and season, and species movement patterns were closely related to their habitat preferences. Based on our results, we argue that comparative population studies of species with different life history traits are necessary to understand the variation in demographic parameters as well as its ecological and evolutionary implications in the face of spatial and climatic environmental variation.

Open versus laparoscopic liver resection of colorectal metastases: a meta-analysis of matched patient populations.

In recent years, the management of colorectal liver metastases (CRLM) has evolved significantly. Laparoscopic liver resection is increasingly being performed, despite a lack of major randomized controlled trial evidence or widespread international consensus. The objective of this review was to compare the short- and long-term outcomes following open and laparoscopic CRLM resection. A systematic review of comparative matched population studies was performed. Evaluated endpoints included surgical outcomes and survival outcomes. Twelve studies were included in this review, reporting on 3095 patients. R0 (negative margins) rates were higher in the laparoscopic CRLM group (89.3% versus 86.9%). In addition, laparoscopic resection was associated with less blood loss (486 mls versus 648 mls, p ≤ 0.0001*) and reduced blood transfusion rates (6.7% vs. 12.2%, OR 2.13, 95% CI 1.08-4.19, p = 0.03*). Major complication rates were higher in the open CRLM group (12.5% vs. 8.1%, OR 1.74, 95% CI 1.30-2.33, p = 0.03*), as was overall hospital length of stay (median 7 versus 5.5days, p = 0.001*). Perioperative mortality was similar between both groups, and there was no significance in 5-year overall survival for open or laparoscopic CRLM resection groups (58% and 61% respectively). Laparoscopic CRLM resection is associated with less blood loss, lower transfusion rates, major complications, and overall hospital length of stay with comparable oncological outcome.

Did population differences in human pelvic form evolve by drift or selection?

Pelvic dimensions differ, on average, among modern human populations. Some recent studies have reported that population differences in pelvic form evolved mainly by neutral processes, without considerable natural selection. This is a surprising claim given the many important functions of the human pelvis. This article re-evaluates this claim through a review of the medical literature and a new analysis of the data from which these results were obtained. We show that variation in modern pelvic form correlates with the risks of obstructed labour, pelvic floor disorders such as incontinence and prolapse, and numerous orthopaedic disorders that impair walking. Comparative population studies also document adaptations of human body form and pelvic dimensions to climatic conditions. However, these various and partly antagonistic selective forces on the human pelvis are not homogeneous across populations. They depend not only on climatic differences, but also on maternal and foetal body size, pelvic floor tissue properties, diet, lifestyle and the resulting metabolic capacities, as well as on obstetric practices and health care, all of which vary across human populations. Given the relatively rapid evolution of polygenic quantitative traits, we propose that pelvic dimensions have evolved different "compromise solutions" in different populations in response to local selective regimes. The results from a reanalysis of a large published global dataset on human pelvic canal dimensions clearly support this view.

Major ascaroside pheromone component asc-C5 influences reproductive plasticity among isolates of the invasive species pinewood nematode.

Pheromones are communication chemicals and regulatory signals used by animals and represent unique tools for organisms to mediate behaviors and make "decisions" to maximize their fitness. Phenotypic plasticity refers to the innate capacity of a species to tolerate a greater breadth of environmental conditions across which it adapts to improve its survival, reproduction, and fitness. The pinewood nematode, Bursaphelenchus xylophilus, an invasive nematode species, was accidentally introduced from North America into Japan, China, and Europe; however, few studies have investigated its pheromones and phenotypic plasticity as a natural model. Here, we demonstrated a novel phenomenon, in which nematodes under the condition of pheromone presence triggered increased reproduction in invasive strains (JP1, JP2, CN1, CN2, EU1, and EU2), while it simultaneously decreased reproduction in native strains (US1 and US2). The bidirectional effect on fecundity, mediated by presence/absence of pheromones, is henceforth termed pheromone-regulative reproductive plasticity (PRRP). We further found that synthetic ascaroside asc-C5 (ascr#9), the major pheromone component, plays a leading role in PRRP and identified 2 candidate receptor genes, Bxydaf-38 and Bxysrd-10, involved in perceiving asc-C5. These results suggest that plasticity of reproductive responses to pheromones in pinewood nematode may increase its fitness in novel environments following introduction. This opens up a new perspective for invasion biology and presents a novel strategy of invasion, suggesting that pheromones, in addition to their traditional roles in chemical signaling, can influence the reproductive phenotype among native and invasive isolates. In addition, this novel mechanism could broadly explain, through comparative studies of native and invasive populations of animals, a potential underlying factor behind of the success of other biological invasions.

Comparative study of existing knee prosthesis with anthropometry of Indian patients and other races, a computer tomography 3D reconstruction-based study

Background: Appropriate component sizing plays an important role in determining the functional outcome following total knee arthroplasty. Comparative studies of different populations have shown significant differences in the anthropometric parameters of knees in different race groups which negates the possibility of using a single sized implant system across different ethnic groups. This study evaluates the dimensions of femoral and tibial articular surfaces of Indian patients and compares the parameters with other ethnic groups and correlates the dimensions with five different commercially available knee systems.Material & Methods: Computerized tomography (CT) scans of contralateral normal knees of patients who underwent the scan for various ailments of the knee were retrieved retrospectively from the hospital database and 3D reconstruction of the images was done. Mediolateral dimensions (fML,tML), Anteroposterior dimensions (fAP, tAP) and aspect ratio (fML/fAP, tML/tAP) of the femur and tibia respectively were calculated and compared with the dimensions of different ethnic groups as well as the femoral and tibial components of five different knee prosthesis systems. ResultsThe average fML in the study group was less than that of Caucasian knees but was marginally larger than other ethnic groups. The fAP, tML and tAP was found to be smaller than all other ethnic groups but a larger femoral aspect ratio was reported than other ethnic groups. Among the implant systems, only NexGen LPS and Scorpio NRG implant femoral components closely matched the femoral dimensions in the study group whereas all implant systems showed significant mismatch with tibial component dimensions when compared to the study populations. ConclusionThis study concludes that the dimensions of Indian knees are different from other ethnic groups and the use of commercially available knee Implants designed based on measurements in Caucasian populations can lead to significant mismatch between implant and resected bone surfaces.

Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb)

The availability of large expressed sequence tag (EST) and whole genome databases of oil palm enabled the development of a data base of microsatellite markers. For this purpose, an EST database consisting of 40,979 EST sequences spanning 27 Mb and a chromosome-wise whole genome databases were downloaded. A total of 3,950 primer pairs were identified and developed from EST sequences. The tri and tetra nucleotide repeat motifs were most prevalent (each 24.75%) followed by di-nucleotide repeat motifs. Whole genome-wide analysis found a total of 245,654 SSR repeats across the 16 chromosomes of oil palm, of which 38,717 were compound microsatellite repeats. A web application, OpSatdb, the first microsatellite database of oil palm, was developed using the PHP and MySQL database (https://ssr.icar.gov.in/index.php). It is a simple and systematic web-based search engine for searching SSRs based on repeat motif type, repeat type, and primer details. High synteny was observed between oil palm and rice genomes. The mapping of ESTs having SSRs by Blast2GO resulted in the identification of 19.2% sequences with gene ontology (GO) annotations. Randomly, a set of ten genic SSRs and five genomic SSRs were used for validation and genetic diversity on 100 genotypes belonging to the world oil palm genetic resources. The grouping pattern was observed to be broadly in accordance with the geographical origin of the genotypes. The identified genic and genome-wide SSRs can be effectively useful for various genomic applications of oil palm, such as genetic diversity, linkage map construction, mapping of QTLs, marker-assisted selection, and comparative population studies.

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals

The gut microbiomes of mammals appear to mirror their hosts’ phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar—three lemur and three non-primate species—that consider genetic, dietary, and ecological predictors of microbiome functionality and composition. Host evolutionary history, indeed, appears to shape gut microbial patterns among both closely and distantly related species. However, we also find that diet—reliance on leaves versus fruit—is the best predictor of microbiome similarity among closely related lemur species, and that host substrate use—ground versus tree—constrains horizontal transmission via incidental contact with feces, with arboreal species harboring far more distinct communities than those of their terrestrial and semi-terrestrial counterparts.

Karyological analysis of the sea cicada Blepharipoda liberate Shen from the Rizhao intertidal zone, China

Blepharipoda liberate Shen is a commercially valuable seafood species that has important ecological significance in Shandong Province, China. Although B. liberate is crustacean, its external characteristics are not entirely those of shrimps or crabs. The question of whether B. liberate is a shrimp or a crab has been debated in recent years. We studied the karyotype of B. liberate by light microscopy using air-drying and spreading methods. We obtained mitotic chromosomal plates from B. liberate larvae, and from adult B. liberate females subsequent to egg-laying. The results revealed that B. liberate has 53 pairs of chromosomes (i.e., n=53 and 2n=106), a characteristic shared with four species of crab. The karyogram of B. liberate consists of 25 metacentric, 14 submetacentric, 11 subtelocentric and 3 telocentric pairs. We did not find any heteromorphosis sex chromosomes. Tissue from larvae, gills and ovaries can be used for chromosomal investigations, and we found similar lampbrush chromosomes in ovary cells. Comparatively speaking, larvae tissue is more practical, and ovary tissue is more suitable for the preparation of lampbrush chromosomes. B. liberate is more closely related to crabs than to shrimps, based on the numbers of chromosomes. The B. liberate karyotype reported here provides a basis for further comparative cytogenetic studies of species populations.

The impact of methylation quantitative trait loci (mQTLs) on active smoking-related DNA methylation changes

BackgroundMethylation quantitative trait loci (mQTLs) are the genetic variants that may affect the DNA methylation patterns of CpG sites. However, their roles in influencing the disturbances of smoking-related epigenetic changes have not been well established. This study was conducted to address whether mQTLs exist in the vicinity of smoking-related CpG sites (± 50 kb) and to examine their associations with smoking exposure and all-cause mortality in older adults.ResultsWe obtained DNA methylation profiles in whole blood samples by Illumina Infinium Human Methylation 450 BeadChip array of two independent subsamples of the ESTHER study (discovery set, n = 581; validation set, n = 368) and their corresponding genotyping data using the Illumina Infinium OncoArray BeadChip. After correction for multiple testing (FDR), we successfully identified that 70 out of 151 previously reported smoking-related CpG sites were significantly associated with 192 SNPs within the 50 kb search window of each locus. The 192 mQTLs significantly influenced the active smoking-related DNA methylation changes, with percentage changes ranging from 0.01 to 18.96%, especially for the weakly/moderately smoking-related CpG sites. However, these identified mQTLs were not directly associated with active smoking exposure or all-cause mortality.ConclusionsOur findings clearly demonstrated that if not dealt with properly, the mQTLs might impair the power of epigenetic-based models of smoking exposure to a certain extent. In addition, such genetic variants could be the key factor to distinguish between the heritable and smoking-induced impact on epigenome disparities. These mQTLs are of special importance when DNA methylation markers measured by Illumina Infinium assay are used for any comparative population studies related to smoking-related cancers and chronic diseases.

Using automated sanding to homogeneously break seed dormancy in black locust (Robinia pseudoacaciaL., Fabaceae)

AbstractPhysical dormancy ofRobinia pseudoacaciaseeds makes it a challenge for scientists and forest managers to obtain a homogeneous germination for larger seed samples. Water imbibition of the seeds can be achieved through manual piercing of the seed coat, but this method remains time consuming and heterogeneous. We tested several ecologically friendly methods to break seed dormancy, including manual pin puncture, water soaking, oven dry-heating (two temperatures) and sanding. Sanding was performed using an automatic grinder to control shaking duration (three durations) and get a homogeneous scraping of the coat. All methods, except dry-heating, resulted in successful dormancy breaking; water soaking was the least efficient method, attaining 57% germination. Sanding proved to be as efficient as puncturing (97%) but long duration sanding (10 or 15 min) could damage cotyledons, which would impede further development of the plant. Short-time sanding (5 min) proved to be the best method to reach high total germination and healthy (undamaged cotyledon) seedlings, and was successfully applied to 500 seeds. The reference puncture method and the automatic sanding were also tested on seeds of nine Fabaceae species and proved to be efficient for some species. Automated sanding can thus be used as a standard to break physical dormancy of black locust or other Fabaceae seeds to allow further comparative studies of plant populations or genotypes.

Strategies for complete plastid genome sequencing.

Plastid sequencing is an essential tool in the study of plant evolution. This high‐copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low‐cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation‐sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short‐range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.