Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae DOI

Abdullah Abdullah,

Furrukh Mehmood, Abdur Rahim

et al.

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(12), P. 7810 - 7826

Published: May 6, 2021

Abstract The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues the phylogeny of due low polymorphism molecular markers. Therefore, suitable polymorphic regions need be identified. Here, we de novo assembled plastomes three species B . oxyodonta , B. tenella balsamifera compared them with 26 other Asteroideae after correction annotations. These quadripartite similar gene content, genome organization, inverted repeat contraction expansion comprising 113 genes, 80 protein‐coding, 29 transfer RNA, 4 ribosomal RNA genes. comparative analysis codon usage, amino acid frequency, microsatellite repeats, oligonucleotide transition transversion substitutions has revealed high resemblance among newly We identified 10 highly nucleotide diversity above 0.02, rps 16‐ trn Q, ycf 1, ndh F‐ rpl 32, pet N‐ psb M, 32‐ L, they may for development robust, authentic, cost‐effective markers barcoding inference Among these regions, five also co‐occurred repeats support use as a proxy identification loci. phylogenetic close relationship between Pluchea within tribe Inuleae. At level, our supports sister Astereae Anthemideae rooted Gnaphalieae, Calenduleae, Senecioneae. results are contradictory recent which reported “Senecioneae Anthemideae” “Astereae Gnaphalieae” or Gnaphalieae Anthemideae, then Senecioneae using nuclear sequences. conflicting signals observed at tribal level plastidt data require further investigation.

Language: Английский

Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae DOI Creative Commons
Yiyong Zhao, Rong Zhang,

Kai-Wen Jiang

et al.

Molecular Plant, Journal Year: 2021, Volume and Issue: 14(5), P. 748 - 773

Published: Feb. 23, 2021

Language: Английский

Citations

168
A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis DOI Creative Commons
Wei‐Chen Huang, Lin Zhang, J. Travis Columbus

et al.

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(4), P. 755 - 777

Published: Jan. 31, 2022

Poaceae (the grasses) includes rice, maize, wheat, and other crops, is the most economically important angiosperm family. also one of largest plant families, consisting over 11 000 species with a global distribution that contributes to diverse ecosystems. are classified into 12 subfamilies, generally strong phylogenetic support for their monophyly. However, many relationships within among tribes and/or subtribes, remain uncertain. To better resolve phylogeny, we generated 342 transcriptomic seven genomic datasets; these were combined datasets provide sequences 357 in 231 genera, representing 45 all subfamilies. Over 1200 low-copy nuclear genes retrieved from datasets, several subsets obtained using additional criteria, used coalescent analyses reconstruct phylogeny. Our results strongly monophyly subfamilies; however, subfamily Puelioideae was separated two non-sister clades, each previously defined tribes, supporting hypothesis places tribe separate subfamily. Molecular clock estimated crown age be ∼101 million years old. Ancestral character reconstruction C3/C4 photosynthesis supports multiple independent origins C4 photosynthesis. These further supported by analysis ppc gene family encodes phosphoenolpyruvate carboxylase, which suggests members three paralogous subclades (ppc-aL1a, ppc-aL1b, ppc-B2) recruited as functional genes. This study provides valuable resources robust framework evolutionary grass

Language: Английский

Citations

102
Phylogenomics and the flowering plant tree of life DOI Open Access
Cen Guo, Yang Luo, Lian‐Ming Gao

et al.

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

Citations

82
The evolutionary history of bees in time and space DOI Creative Commons
Eduardo A. B. Almeida, Silas Bossert, Bryan N. Danforth

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(16), P. 3409 - 3422.e6

Published: July 27, 2023

Language: Английский

Citations

48
Development and evolution of the Asteraceae capitulum DOI Creative Commons
Teng Zhang, Paula Elomaa

New Phytologist, Journal Year: 2024, Volume and Issue: 242(1), P. 33 - 48

Published: Feb. 15, 2024

Asteraceae represent one of the largest and most diverse families plants. The evolutionary success this family has largely been contributed to their unique inflorescences, capitula that mimic solitary flowers but are typically aggregates multiple florets. Here, we summarize recent molecular genetic level studies have promoted our understanding development evolution capitula. We focus on new results patterning enlarged meristem resulting in iconic phyllotactic arrangement florets Fibonacci numbers spirals. also current networks regulating characteristic reproductive traits such as floral dimorphism differentiation highly specialized organs. So far, developmental still limited a very narrow selection model species. Along with advancements genomics phylogenomics, its relatives provide an outstanding clade for extended evo-devo exploit morphological diversity underlying translate knowledge breeding key crops family.

Language: Английский

Citations

17
Design of CoQ10 crops based on evolutionary history DOI Creative Commons

Jing-Jing Xu,

Lei Yuan,

Xiaofan Zhang

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

3
Pollen Diversity in the Tribe Cardueae (Asteraceae) and Its Taxonomic Significance DOI Open Access
Neda Atazadeh, Farrokh Ghahremaninejad

Microscopy Research and Technique, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

ABSTRACT The Cardueae with about 74 genera and 2500 species is one of the largest tribes family Asteraceae. taxonomy complicated unresolved, as it contains most diverse genera. main distribution centers are in eastern western Mediterranean, Irano‐Turanian region, central Asia, North Africa. Using pollen morphology can be a useful tool for identification delimitation taxa. Therefore, current study aims to describe types tribe based on features. Furthermore, addresses relationships among palynological features well morphology. Pollen 39 distributed 28 was examined by scanning electron microscopy. In present study, statistical analyses various clustering ordination methods were provided data. Based these results, members nine subtribes showed overlap This extreme heterogeneity taxa could attributed large number their high morphological diversity. However, suitable distinguished taxonomic differentiation Cardueae, including shape, size, polar axis equatorial diameter ratio [P/E], exine sculpture, spine size. Consequently, six identified studied Cardueae.

Language: Английский

Citations

2
Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications DOI Creative Commons
Caifei Zhang, Taikui Zhang, Federico Luebert

et al.

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 37(11), P. 3188 - 3210

Published: June 26, 2020

Abstract Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number important crops. Despite their biological prominence value to humans, deep asterid phylogeny has not been fully resolved, evolutionary landscape underlying radiation remains unknown. To resolve phylogeny, we sequenced 213 transcriptomes/genomes combined them with other data sets, representing all accepted orders nearly families asterids. We show supported monophyly asterids, Berberidopsidales as sister except Icacinales, Aquifoliales, Bruniales, Icacinaceae Ehretiaceae. Novel taxon placements benefited from expanded sampling living collections botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous here likely due limited could be addressed in future relevant additional taxa. Using our well-resolved reference, divergence time estimates support an Aptian (Early Cretaceous) origin asterids before Cretaceous–Paleogene boundary. Ancestral state reconstruction at family level suggests that ancestor was woody terrestrial plant simple leaves, bisexual, actinomorphic flowers free petals anthers, superior ovary style, drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs Berberidopsidales, four suprafamilial seven familial/subfamilial WGDs. Our results advance understanding numerous novel insights into diversification evolution.

Language: Английский

Citations

122
Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation DOI Creative Commons
Caifei Zhang, Chien‐Hsun Huang, Mian Liu

et al.

Journal of Integrative Plant Biology, Journal Year: 2021, Volume and Issue: 63(7), P. 1273 - 1293

Published: Feb. 10, 2021

Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) largest and most diverse plant families, but its species diversity concentrated in a few subfamilies, providing an opportunity study affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes genomes produced phylogeny with strong support for monophyly Asteraceae subfamilies tribes. This provides reference detecting changes diversification rates possible diversity, which include global climate shifts, whole-genome duplications (WGDs), morphological evolution. origin was estimated at ~83 Mya, having diverged before Cretaceous-Paleocene boundary. supported existence 41 WGDs Asteraceae. Changes herbaceousness capitulescence multiple flower-like capitula, often distinct florets scaly pappus/receptacular bracts, are associated upshifts rate. might have contributed survival early by new genetic materials transitions. resulting competitive advantage adapting different niches would increased biodiversity

Language: Английский

Citations

88
Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications DOI Creative Commons
Goon-Bo Kim,

Chae Eun Lim,

Jin-Seok Kim

et al.

BMC Genomics, Journal Year: 2020, Volume and Issue: 21(1)

Published: June 22, 2020

Abstract Background Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification taxa, however, has been hampered by insufficient diagnostic morphological characteristics frequent natural hybridization. Development novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues is significant challenge. Results To establish molecular basis comparative phylogenomic analysis , we newly determined 19 chloroplast genome (plastome) sequences 18 Asia, de novo-assembled annotated the plastomes two using publicly available Illumina reads, compared them 11 reported previously. were 150,858–151,318 base pairs (bp) length harbored 87 protein-coding genes, 37 transfer RNAs, 8 ribosomal RNA genes conserved order orientation. Evolutionary analyses whole 80 non-redundant revealed noncoding trnH-psbA spacer was highly variable size nucleotide sequence both between within whereas coding accD ycf1 under weak positive selection relaxed selective constraints, respectively. Phylogenetic based on maximum likelihood Bayesian inference yielded five groups clustered monophyletic subgenus Dracunculus paraphyletic suggesting can be as infer haplotypes taxa. Additionally, hotspots enabled development potentially applicable across family Asteraceae high discriminatory power. Conclusions complete sufficiently polymorphic super-barcodes this genus. It will facilitate new study relationships species Asteraceae.

Language: Английский

Citations

72