Ploidy Research Articles

Revolutionizing Rice Grain Quality: A Holistic Review Integrating Conventional and Molecular Approaches

This review mainly focuses on the rice grain quality based on which rice varieties are distinguished into several quality classes like, physical quality, eating and cooking quality and nutritional quality. The rice breeding programme needs to focus on the development of nutrient-dense rice for value addition, helping in reducing malnutrition and Vitamin-A deficiency (VAD). There is enough scope to enhance the nutritional and cooking quality in small and medium grain rice germplasm by bringing them into the breeding programme through Fe and Zn and Vitamin-A biofortification, aided with molecular techniques. Many studies have been conducted to find out the quantitative trait locus (QTL) for enhancing the quality of grain. The QTL qBRR5 and qBRR3 are responsible for brown rice grain width and length found on chromosome 5 and on chromosome number 3, respectively and for head rice on chromosome number 1, 5, and 6. The QTLs present on chromosomes 3, 5, and 6 are responsible for head rice recovery, chalky appearance of rice grain as well as grain size and shape. The gene Wx, located on chromosome 6 linked with the QTL qAC6 regulate amylose content and gel consistency. The QTL SSIIa on chromosome 6, control both the amylopectin and gelatinization temperature. The QTLs for Fe and Zn content in rice grain are located on chromosome 2, 3, 8, 11 and 12. Development of “Golden rice” and innovations with Arabidopsis genes can significantly enhance β-carotene levels and address Vitamin-A deficiency, while RNAi techniques improve storage quality.

Phenotypic continuum and poor intracytoplasmic sperm injection intracytoplasmic sperm injection prognosis in patients harboring HENMT1 variants.

Small RNAs interacting with PIWI (piRNAs) play a crucial role in regulating transposable elements and translation during spermatogenesis and are essential in male germ cell development. Disruptions in the piRNA pathway typically lead to severe spermatogenic defects and thus male infertility. The HENMT1 gene is a key player in piRNAs primary biogenesis and dysfunction of HENMT1 protein in meiotic and haploid germ cells resulted in the loss of piRNA methylation, piRNA instability, and TE de-repression. Henmt1-knockout mice exhibit a severe oligo-astheno-teratozoospermia (OAT) phenotype, whereas patients with HENMT1 variants display more severe azoospermia phenotypes, ranging from meiotic arrest to hypospermatogenesis. Through whole-exome sequencing (WES) of infertile patient cohorts, we identified two new patients with variants in the HENMT1 gene presenting spermatozoa in their ejcaulate, providing us the opportunity to study spermatozoa from these patients. Investigate the spermatozoa of two patients harboring an HENMT1 variant to determine whether or not these scarce spermatozoa could be used with assisted reproductive technologies. HENMT1 variants identified by WES were validated through Sanger sequencing. Comprehensive semen analysis was conducted, and sperm cells were subjected to transmission electron microscopy for structural examination, in situ hybridization for aneuploidy assessment, and aniline blue staining for DNA compaction status. Subsequently, we assessed their suitability for in vitro fertilization using intracytoplasmic sperm injection (IVF-ICSI). Our investigations revealed a severe OAT phenotype similar to knockout mice, revealing altered sperm concentration, mobility, morphology, aneuploidy and nuclear compaction defects. Multiple IVF-ICSI attempts were also performed, but no live births were achieved. We confirm the crucial role of HENMT1 in spermatogenesis and highlight a phenotypic continuum associated with HENMT1 variants. Unfortunately, the clinical outcome of these genetic predispositions remains unfavorable, regardless of the patient's phenotype. The presence of spermatozoa is insufficient to anticipate ICSI pregnancy success in HENMT1 patients.

Preconceptional thyroid-stimulating hormone affects antral follicle count rather than pregnancy outcomes in patients with first in vitro fertilization/intracytoplasmic sperm injection cycle

Objective: To study the effects of preconceptional thyroid-stimulating hormone (TSH) levels on antral follicle count (AFC) and pregnancy outcomes in a first in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycle. Methods: A retrospective cohort study was conducted to explore the effects of preconceptional TSH levels on AFC and pregnancy outcomes in 1340 patients. The patients were divided into three groups: group 1, 0.55≤ TSH <2.5 uIU/mL (n = 868); group 2, 2.5≤ TSH <4.0 uIU/mL (n = 334); and group 3, TSH ≥4.0 uIU/mL (n = 138). Results: There were significant differences in AFC (P = 0.002), number of zygotes (P = 0.008), and fertilization rate (P = 0.015) among the three groups. Among the three groups, there were no obvious differences in live birth (P = 0.559), high-quality embryo (P = 0.108), or clinical pregnancy (P = 0.939) rates. Binary logistics regression analysis showed that TSH correlated with AFC when TSH was ≥4 uIU/mL (P = 0.033); however, TSH levels had no effect on live birth or clinical pregnancy rate. Conclusions: Although the preconceptional TSH level negatively related with AFC, number of zygotes, and fertility rate, especially when TSH was >4 uIU/mL, TSH was not an independent factor on the live birth rate among fertile women undergoing their first IVF/ICSI-embryo transfer treatment. The effect of TSH levels on couples undergoing assisted reproductive technology requires further investigation.

Conditions for establishing fin primary cell cultures in a wide range of ray-finned fishes.

Ray-finned fishes (Actinopterygii) represent the most diverse vertebrate lineage that show extensive variations in physiology, ways of life, and adaptations to marine and freshwater environments, and several species have been established as biological research models. The in vitro culture of cells is fundamental for several fields of biological research, being an alternative for studies that use animals. Hundreds of fish cell lines have been established using specific methods for each cell type and species. Here is described a protocol which can be used commonly for obtaining cell cultures from the caudal fin of a wide range of ray-finned fishes including marine and freshwater species. Conditions for sample collection, microbial disinfection, tissue dissociation, plating and incubation, cryopreservation and thawing, and karyotyping are described in detail. Primary cell cultures were developed for 20 species grouped into 12 different orders. Eleven of these species have been cultivated in vitro for the first time. In the beginning, the fish cell cultures showed different capacities of proliferation among them; however throughout the passages, most cultures began to have a similar proliferation rate. Throughout the passages, it was noticed that cells similar to fibroblasts began to predominate. The great proliferative ability of these cultures reveals their potential to become cell lines. The culture of A. mexicanus, for example, has been proliferating for months and is already in its 65th passage. Moreover, these cell cultures showed conserved diploid chromosome numbers in comparison with in vivo descriptions which suggest these cultures have stable karyotypes. Therefore, these cultures have potential to be used in several fields, such as toxicology, cytogenetics, genomics, pathology, immunology, cellular agriculture, and conservation, and this method has the potential to be expanded to species not yet tested, as well as to other organs.

Spindle architecture constrains karyotype evolution

The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cell’s chromosomes in a carefully coordinated process. However, chromosome numbers vary dramatically between genomes, even on short evolutionary timescales. We sought to understand how the mitotic machinery senses and responds to karyotypic changes by using a series of budding yeast strains in which the native chromosomes have been successively fused. Using a combination of cell biological profiling, genetic engineering and experimental evolution, we show that chromosome fusions are well tolerated up until a critical point. Cells with fewer than five centromeres lack the necessary number of kinetochore-microtubule attachments needed to counter outward forces in the metaphase spindle, triggering the spindle assembly checkpoint and prolonging metaphase. Our findings demonstrate that spindle architecture is a constraining factor for karyotype evolution.

Chromosomal Characterization of Five Medicinally Significant Phyllanthus Species in Bangladesh by DNA Base-Specific Fluorochrome Banding Technique

ABSTRACT Five Phyllanthus species were characterized using a fluorochrome chromosome banding technique with CMA and DAPI. This genus displayed a range of somatic chromosomal counts, including 2n = 2x = 26 (diploid) in P. acidus, P. niruri, and P. reticulatus; 2n = 6x = 48 (hexaploid) in P. urinaria; and 2n = 10x = 100 (decaploid) in P. emblica (wild and cultivated varieties), which exhibited a multi-basic chromosome number. The centromeric and terminal regions of the chromosomes contained most of the CMA and DAPI bands, indicating that GC- and AT-rich repeats had accumulated in these locations. The diversity based on the heterochromatin distribution patterns made it possible to use the CMA and DAPI banding approaches to analyze and characterize these five Phyllanthus species.

Naturally occurring horse model of miscarriage reveals temporal relationship between chromosomal aberration type and point of lethality

Chromosomal abnormalities are a common cause of human miscarriage but rarely reported in any other species. As a result, there are currently inadequate animal models available to study this condition. Horses present one potential model since mares receive intense gynecological care. This allowed us to investigate the prevalence of chromosomal copy number aberrations in 256 products of conception (POC) in a naturally occurring model of pregnancy loss (PL). Triploidy (three haploid sets of chromosomes) was the most common aberration, found in 42% of POCs following PL over the embryonic period. Over the same period, trisomies and monosomies were identified in 11.6% of POCs and subchromosomal aberrations in 4.2%. Whole and subchromosomal aberrations involved 17 autosomes, with chromosomes 3, 4, and 20 having the highest number of aberrations. Triploid fetuses had clear gross developmental anomalies of the brain. Collectively, data demonstrate that alterations in chromosome number contribute to PL similarly in women and mares, with triploidy the dominant ploidy type over the key period of organogenesis. These findings, along with highly conserved synteny between human and horse chromosomes, similar gestation lengths, and the shared single greatest risk for PL being advancing maternal age, provide strong evidence for the first animal model to truly recapitulate many key features of human miscarriage arising due to chromosomal aberrations, with shared benefits for humans and equids.

Species of the Sections Hedysarum and Multicaulia of the Genus Hedysarum (Fabaceae): Taxonomy, Distribution, Chromosomes, Genomes, and Phylogeny.

The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum.

Genomic insights into cytokinin oxidase/dehydrogenase (CKX) gene family, identification, phylogeny and synteny analysis for its possible role in regulating seed number in Pigeonpea (Cajanus cajan (L.) Millsp.)

Cytokinin oxidase/dehydrogenase (CKX) regulates cytokinin levels in plants which are vital for plant growth and development. However, there is a paucity of evidence regarding their role in controlling embryo/seed development in pigeonpea. This comprehensive study provides information on the identification and characterization of CKX genes in pigeonpea. A genome-wide analysis identified 18 CKX genes, each with distinct structure, expression patterns, and possible diverse functions. Domain analysis revealed the presence of the sequences including FAD and CK-Binding domain, and subcellular localization analysis showed that almost 50 % of them reside within the nucleus. They were observed to be located unevenly on chromosome numbers 2, 4, 6, 7, and 11 with a majority of them present on the scaffolds. The 8 homologous pairs and various orthologous gene pairs provided further insights into their evolution pattern. Further, SNP/Indels variation in CKX genes and haplotype groups among contrasting genotypes for SNPP (seed number per pod) were analyzed. Spatiotemporal expression analysis revealed the significant expression pattern of CcCKX15, CcCKX17, and CcCKX2 in genotypes carrying low SNPP reiterating their possible role as negative regulators. These genes can be potential targets to undertake seed and biomass improvement in pigeonpea.

MEILB2-BRME1 forms a V-shaped DNA clamp upon BRCA2-binding in meiotic recombination

DNA double-strand break repair by homologous recombination has a specialised role in meiosis by generating crossovers that enable the formation of haploid germ cells. This requires meiosis-specific MEILB2-BRME1, which interacts with BRCA2 to facilitate loading of recombinases onto resected DNA ends. Here, we report the crystal structure of the MEILB2-BRME1 2:2 core complex, revealing a parallel four-helical assembly that recruits BRME1 to meiotic double-strand breaks in vivo. It forms an N-terminal β-cap that binds to DNA, and a MEILB2 coiled-coil that bridges to C-terminal ARM domains. Upon BRCA2-binding, MEILB2-BRME1 2:2 complexes dimerize into a V-shaped 2:4:4 complex, with rod-like MEILB2-BRME1 components arranged at right-angles. The β-caps located at the tips of the MEILB2-BRME1 limbs are separated by 25 nm, allowing them to bridge between DNA molecules. Thus, we propose that BRCA2 induces MEILB2-BRME1 to function as a DNA clamp, connecting resected DNA ends or homologous chromosomes to facilitate meiotic recombination.

The establishment of pulp polyp-derived mesenchymal stem cells with normal karyotype

Background/PurposePulp polyp is often eliminated as dental waste. Pulp polyp cells were reported to have high proliferation activity which might be comprised of stem cells. However, little has been known on the presence of stem cells in the pulp polyp. Moreover, pulp polyp cells might contain chromosomal abnormality. The present study was conducted to investigate the presence of pulp polyp stem cells, which could later be propagated and confirmed as normal/non-pathogenic cells using karyotype analysis. Materials and methodsCollected pulp polyps were minced, enzymatically digested, and cultured. Expression of mesenchymal stem cell (MSC) markers on pulp polyp cells were analyzed using flow cytometry. Multilineage differentiation capacity was assessed by culturing the cells in osteogenic, chondrogenic, and adipogenic differentiation media. Genomic stability of the cells was evaluated with G-banded and molecular karyotype analyses. ResultsPulp polyp cells appeared as fibroblasts-like cells. The cells were positive for cluster of differentiation (CD)105, CD90, and CD73, and negative for CD45, CD34, CD11b, CD19, and human leukocyte antigen (HLA)-DR. The cells were capable of osteogenic, chondrogenic, and adipogenic differentiation. G-banded karyotype analysis showed that there was no abnormality in the number or structure of chromosomes in pulp polyp-derived MSCs (PP-MSCs). Molecular karyotype analysis revealed that all copy number variations identified in PP-MSCs were not pathogenic. ConclusionPP-MSCs, which fulfill the minimal criteria for MSCs and are proven to have normal karyotype, have been successfully established. PP-MSCs might be a promising and safe candidate that can be considered for pulp-dentin complex regeneration.

Current and Emerging Biomarkers: Impact on Risk Stratification for Neuroblastoma.

Neuroblastoma has heterogenous clinical presentations that are reflected by several well-defined clinical factors and biomarkers. Combinations of these clinical and biologic prognostic factors have been used for decades to generate classifiers to stratify patients into risk groups (low, intermediate, and high), which in turn are used to inform and tailor treatment as reported in the new NCCN Clinical Practice Guidelines in Oncology for Neuroblastoma. Risk classification uses clinical features, such as age and tumor stage, along with the most significant prognostic tumor biomarkers, including histologic features (differentiation and mitosis-karyorrhexis index), MYCN amplification status, chromosomal copy number alterations (segmental or numerical), and ploidy (DNA content). Recent next-generation sequencing approaches have identified additional tumor-specific genetic factors that have potential roles as prognostic and predictive biomarkers. These emerging biomarkers include telomerase maintenance mechanisms, such as telomerase reverse transcription (TERT) expression and alternative lengthening of telomeres (ALT) status. Somatic alterations of genes, including mutations in the anaplastic lymphoma kinase gene ALK, detected in >10% of patients with newly diagnosed disease, have both prognostic and predictive roles in determining eligibility for targeted therapies (eg, ALK tyrosine kinase inhibitors). In addition to diagnostic tumor-derived biomarkers, significant effort is being directed toward identification of markers to predict response to chemotherapy and immunotherapies. With the increasing use of GD2-containing immunotherapy regimens, efforts are aimed at identifying host or tumor microenvironment immune correlatives that can serve as predictive biomarkers. Understanding the potential role of liquid biopsies as biomarkers during and following treatment, including sequential circulating tumor DNA or tumor-specific mRNA transcripts, is expected to enhance the ability to predict recurrences and also inform understanding of tumor evolution and therapy resistance. These and other emerging biomarkers will lead to refinement and optimization of future neuroblastoma risk classification systems.

Cytogenics, morphology and viability of Borreria spinosa (Rubiaceae) pollen grains

Introduction: Borreria spinosa is a herbaceous plant considered a weed in agricultural crops, although it also has potential in apiculture. Despite its agronomic importance, its cytogenetic and palynological traits are poorly known. Objective: To do the cytogenetic characterization of B. spinosa, describe the morphology of its pollen grains, and estimate their potential viability. Methods: We collected plant material in Santiago del Estero, Argentina, in May 2017 and used classical methods (8-hydroxyquinoline and Farmer for mitosis and meiosis; viability with Müntzing; pollen morphology with nonacetolysed and acetolysed techniques, and SEM). Results: B. spinosa has a chromosome number of 2n = 56, with a karyotype of 46 m + 10 sm. Meiotic abnormalities mainly include chromosomes outside the equatorial plate, lagging chromosomes, and cytomixis. Pollen grains are small to medium-sized, suboblate to oblate-spheroidal, with a viability of 70%. This is a tetraploid species, most chromosomes are metacentric or submetacentric; and it has irregular meiotic behavior and cytomixis, with concomitant low viability in pollen grains. Conclusion: In B. spinose, pollen grains have similar characteristics to other species of the genus Borreria.

Complete characterization and comparative analysis of the mitochondrial genome of Indian tasar silkworm Antheraea mylitta (Lepidoptera: Saturniidae) and phylogenetic implications

The Indian tasar silkworm Antheraea mylitta (A. mylitta) is an economically important silkmoth and is native to tropical India. Our current research has deciphered the mitochondrial genome (mitogenome) of A. mylitta by recovering the complete genome sequence from the NCBI-SRA database and comparing it with other mitogenomes from the order Lepidoptera. The mitogenome is a double-stranded circular molecule spanning 15,354 bp with an A + T content of roughly 80.4%. It consists of a total of 37 genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), along with a 337 bp long control region. The arrangement of PCGs is similar to other Lepidoptera mitogenomes, with the exception of Cox1 and Cox2, which have different initiation codons. The control region of A. mylitta contains a conserved five bp ATAGA motif as seen in other Antheraea species. Phylogenetic analysis supports previous morphological hypotheses that Bombycoidea, Noctuoidea, Geometroidea, Papilionoidea, and Torticoidea are monophyletic. The divergence time analysis of 13 protein-coding genes reported that A. mylitta diverged from the last common ancestor ∼ 23 million years ago. As per our knowledge, this is the first documented record of the entire mitogenome of A. mylitta.

THE CHEMISTRY OF THE GENUS STEVIA (ASTERACEAE)

The morphological characteristic and the cytological studies made on the genus Stevia are described. Take into aécount that the chemistry of the genus might be useful for a more precise delimitation of their species; to establish relationships between chemistry, morphology and chromosomic number and to establish relationships with other genera of the tribe, the review of the isolated compounds from 54 species and 8 varieties already studied up 1997 is made.

Fetal agenesis of corpus callosum: chromosomal copy number abnormalities and postnatal follow-up

ObjectiveAgenesis of the corpus callosum (ACC) is an anomaly that can occur in fetuses during pregnancy. However, there is currently no treatment for fetal ACC. Therefore, we conducted a retrospective analysis of obstetric outcomes of fetal ACC to explore the relationship between fetal ACC phenotypes and chromosomal copy number abnormalities.Methods and resultsAmniotic fluid or umbilical cord blood were extracted from pregnant women with fetal ACC for karyotype analysis and chromosomal microarray analysis (CMA). Among the 48 fetuses with ACC, 22 (45.8%, 22/48) had isolated ACC, and 26 (54.2%, 26/48) had non-isolated ACC. Chromosomal abnormalities were detected via karyotype analysis in four cases. In addition to the four cases of pathogenic copy number variations (CNVs) detected using karyotype analysis, CMA revealed two cases of pathogenic CNVs with 17q12 microduplication and 16p12.2 microdeletion. The obstetric outcomes of 26 patients with non-isolated ACC were followed up, and 17 chose to terminate the pregnancy. In addition, seven of the nine cases with non-isolated ACC showed no obvious abnormality during postnatal follow-up, whereas only one case with normal CMA showed an abnormal phenotype at six months. Of the 22 patients with isolated ACC, six chose to terminate the pregnancy. Postnatal follow-up of 16 isolated ACC cases revealed only one with benign CNV, presenting with intellectual disability.ConclusionPregnant women with fetal ACC should be offered prenatal CMA, particularly non-isolated ACC. Patients with ACC should undergo prolonged postnatal follow-up, and appropriate intervention should be provided if necessary.

Metastatic Leiomyoma With Malignant Transformation Harboring RAB2A-PLAG1 Fusion-A Case Report and Review With Molecular Analysis.

Metastasizing leiomyoma is a rare condition characterized by the development of benign-appearing smooth muscle neoplasms at extrauterine sites in patients with a history of uterine leiomyoma. These lesions occur most commonly in the lung, with the abdominopelvic and mediastinal lymph nodes being other reported sites. Malignant transformation of metastasizing leiomyoma is extremely rare, with only a few cases described in the literature. We describe a case of metastasizing leiomyoma with malignant transformation in a middle-aged Asian lady, who developed pulmonary metastatic foci 12 years after surgical excision of the original uterine leiomyomata. Molecular analysis showed a common RAB2A-PLAG1 fusion gene and identical single nucleotide variants in both tumor foci, with significantly more pronounced segmental chromosomal copy number variations in one focus showing high-grade features. A comprehensive review of the literature lends support to the hypothesis that the original leiomyomata and the metastatic foci are clonally related, with high-grade features being associated with more complex genomic signatures.

Genome size and chromosome number variation in sugarcane (Saccharum spp.) families and phenotypically contrasting Saccharum genotypes

AbstractModern sugarcane (Saccharum spp.) cultivars originated from an intricate hybridization process, resulting in complex polyploid and aneuploid genomes. Flow cytometry (FCM), which has emerged as a precise and fast method for research on genome size in plants, has potential to unveil key aspects of sugarcane cytogenetics. In this study, FCM probes were conducted to estimate 2C DNA content in 175 Saccharum genotypes embracing phenotypically contrasting canes (commercial cultivars, energy‐cane hybrids, and a Saccharum spontaneum accession) and full‐sib sugarcane families. FCM‐mediated DNA content estimates exhibited high accuracy in predicting chromosome numbers, offering a time‐efficient alternative to classical cytogenetic procedure. Low‐magnitude correlations detected between DNA content and phenotypic traits suggest that indirect selection of agronomic traits using FCM‐mediated DNA content estimates may not be efficient. DNA content variation patterns in sugarcane families varied according to the crossing, and revealed transgressive variations associated with rampant aneuploidy. Altogether, the findings uncover that loss or gain of genetic material constitutes a source of high genetic variability that may substantially impact on crop breeding.

Chromosome Mapping of Ribosomal DNA Clusters in Four Leaf-cutting Ant Species of the Genus Acromyrmex, with Description of a Triploid Individual in A. laticeps

The increase of cytogenetic data in the leaf-cutting genus Acromyrmex has shown interesting contributions to the evolutionary and taxonomic approaches, including the creation of a new genus and the description of chromosomal patterns allowing comparative studies within Acromyrmex as well as between this genus and other similar taxa. The conserved chromosome number in Acromyrmex is a notable feature, with some distinguishable chromosomes among the species. In this study, we describe the diploid karyotype of Acromyrmex laticeps in addition to an individual with all the metaphases triploids, suggesting a triploid individual. To the best of our knowledge, this is the first report of polyploidy in a fungus-growing ant. Furthermore, we mapped 18S ribosomal DNA on the chromosomes of A. laticeps and three other Acromyrmex species. Among them, three species showed the ribosomal DNA cluster pattern observed in other previously studied members of this genus, with a terminal location in the largest subtelocentric pair. Meanwhile, Acromyrmex balzani had these ribosomal DNA clusters in its entire short arm. The role of triploidy in ant evolution has also been discussed. The increase in chromosomal data of leaf-cutting ants may provide significant insights into the evolution of this peculiar ant group.

Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline.

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise two large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.