Chromosome-scale reference genome of Pectocarya recurvata, a species with one of the smallest genome sizes in Boraginaceae DOI Creative Commons
Poppy C. Northing, Jessie A. Pelosi, D. Lawrence Venable

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

ABSTRACT Premise Pectocarya recurvata (Boraginaceae), a native species of the Sonoran Desert, has served as an important model system for suite ecological and evolutionary studies. Despite its relevance eco-evolutionary model, no reference genome assemblies in Cynoglossoideae subfamily have been published. Methods Using PacBio HiFi sequencing, we assembled P. annotated coding regions with full-length transcripts from Iso-Seq transcriptome library. We assessed completeness BUSCO used flow cytometry K-mer analysis to estimate size . Results The chromosome-scale assembly was 216.0 Mbp long contig N50 12.1 Mbp. Our included 12 primary contigs bounded by telomeres at all ends but one, consistent chromosomes documented species. covered 158.3 contained 30,655 predicted genes. measured haploid same population 386.5 Mbp, among smallest Boraginaceae. Genomic analyses suggested that this may reflect recent autotetraploid, such diploid would be even smaller similar size. Discussion annotation provide high-quality genomic resource sparsely represented area Angiosperm phylogeny. new will enable future ecophysiology, biogeography, phylogenetics research.

Language: Английский

The Role of Meiotic Drive in Chromosome Number Disparity Between Heterosporous and Homosporous Plants DOI
Sylvia P. Kinosian, Michael S. Barker

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

ABSTRACT In vascular plants, heterosporous lineages typically have fewer chromosomes than homosporous lineages. The underlying mechanism causing this disparity has been debated for over half a century. Although reproductive mode identified as critical to these patterns, the symmetry of meiosis during sporogenesis overlooked potential cause difference in chromosome numbers. most megasporogenesis is asymmetric, meaning one four meiotic products survives become egg. Comparatively, symmetric and all survive. important because asymmetric enables drive associated genomic changes, while cannot lead drive. Meiotic deviation from Mendelian inheritance where genetic elements are preferentially inherited by surviving egg cell, can profoundly impact (and genome) size, structure, number. Here we review how impacts number evolution lack plants their genomes, explore future approaches understand role on across land plants.

Language: Английский

Citations

0
SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics DOI Creative Commons
Rengang Zhang,

Hong-Yun Shang,

Richard I. Milne

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(7)

Published: April 10, 2025

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods identifying face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable robust approach, based on Orthology Index (OI), to effectively identify Our evaluation across large-scale empirical dataset diverse polyploidization events demonstrated high reliability robustness OI method. Simulation-based benchmarks further validated accuracy our method, showing its superior performance against existing wide range scenarios. Additionally, explored broad applications plant genomes, including inference polyploidy, identification reticulation, phylogenomics. conclusion, offers robust, interpretable, approach synteny, facilitating more efficient analyses genomics.

Language: Английский

Citations

0
Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy DOI Open Access
Michael S. Barker, Yuannian Jiao, Kelsey L. Glennon

et al.

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(8)

Published: Aug. 1, 2024

Abstract All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant (Wood 2009; Barker 2016a). A major implication these discoveries is that, to appreciate the evolution diversity, we need understand fundamental biology polyploids diploidization. This broadly by our community there a continued, growing interest in polyploidy research topic. Over past 25 years, sequencing analysis genomes has revolutionized understanding importance speciation land plants.

Language: Английский

Citations

2
Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes DOI Creative Commons
Rengang Zhang,

Hong-Yun Shang,

Richard I. Milne

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 23, 2024

Abstract With the explosive growth of whole-genome datasets, accurate detection orthologous synteny has become crucial for reconstruction evolutionary history. However, currently available methods identification have great limitations: are difficult to scale with varying polyploidy histories, and removal out-paralogy is challenging. In this study, we developed a scalable robust approach, Orthology Index ( OI ), identify synteny. Our evaluation large-scale dataset diverse polyploidization events demonstrated that technique highly reliable. This discovery highlights as potentially unified criterion synteny, further validated using simulation-based benchmarks. addition, explore its broad applications in reconstructing histories plant genomes, including inference polyploidy, reticulation, phylogenomics. conclusion, offers robust, interpretable, approach identifying significantly enhancing our analytical prowess genomics.

Language: Английский

Citations

1
Chromosome-scale reference genome of Pectocarya recurvata, a species with one of the smallest genome sizes in Boraginaceae DOI Creative Commons
Poppy C. Northing, Jessie A. Pelosi, D. Lawrence Venable

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

ABSTRACT Premise Pectocarya recurvata (Boraginaceae), a native species of the Sonoran Desert, has served as an important model system for suite ecological and evolutionary studies. Despite its relevance eco-evolutionary model, no reference genome assemblies in Cynoglossoideae subfamily have been published. Methods Using PacBio HiFi sequencing, we assembled P. annotated coding regions with full-length transcripts from Iso-Seq transcriptome library. We assessed completeness BUSCO used flow cytometry K-mer analysis to estimate size . Results The chromosome-scale assembly was 216.0 Mbp long contig N50 12.1 Mbp. Our included 12 primary contigs bounded by telomeres at all ends but one, consistent chromosomes documented species. covered 158.3 contained 30,655 predicted genes. measured haploid same population 386.5 Mbp, among smallest Boraginaceae. Genomic analyses suggested that this may reflect recent autotetraploid, such diploid would be even smaller similar size. Discussion annotation provide high-quality genomic resource sparsely represented area Angiosperm phylogeny. new will enable future ecophysiology, biogeography, phylogenetics research.

Language: Английский

Citations

0