New Phytologist最新文献_第3页

Bamboo mosaic virus-mediated transgene-free genome editing in bamboo

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-06 DOI: 10.1111/nph.20386

Lin Wu, Jun Yang, Yuying Gu, Qianyi Wang, Zeyu Zhang, Hongjue Guo, Liangzhen Zhao, Hangxiao Zhang, Lianfeng Gu

Introduction

The common method of delivering CRISPR/Cas reagents for genome editing in plants involves Agrobacterium-mediated transformation or preassembled CRISPR/Cas9 ribonucleoprotein complex delivery (Woo et al., 2015; Toda et al., 2019; Ye et al., 2020). These methods require labor-intensive and time-consuming plant tissue culture processes (Huang et al., 2022). Unfortunately, most plants exhibit extremely low efficiency in callus induction and regeneration; these technical challenges greatly hinder the application of genome editing. Recent developments in plant RNA virus-based expression vectors (Ma et al., 2020; Chen et al., 2022) provide a convenient, efficient, and cost-effective way for DNA-free genome editing in plants, leveraging the fact that virus RNA does not integrate into the genome. However, the stability of virus vectors is negatively correlated with the size of the inserted foreign genes. Consequently, achieving efficient expression of Streptococcus pyogenes Cas9 (SpCas9, c. 4.2 kb) by virus-based vectors remains challenging. Most reported viruses capable of delivering Cas9 proteins are negative-strand RNA viruses (Ma et al., 2020; Liu et al., 2023; Zhao et al., 2024), with only a few positive-strand RNA viruses identified (Uranga et al., 2021; Lee et al., 2024). Thus, delivering virus-based sgRNA vectors to plants overexpressing Cas9 is the most commonly used strategy (Ali et al., 2015; Jiang et al., 2019; Li et al., 2021). However, it is difficult to use this method to generate a Cas9-free mutant by crossing with wild-type (WT) plants with long flowering cycles, such as bamboo (Ye et al., 2017). Bamboo mosaic virus (BaMV) has a typical flexible filamentous virion structure with the positive-sense single-stranded RNA genome (Hsu et al., 2018). The BaMV-mediated expression system can effectively drive the expression of large foreign gene fragments (Jin et al., 2023). For the first time, we developed a BAMV-mediated Cas protein and sgRNA delivery system in WT Nicotiana benthamiana and bamboo. This approach enables targeted gene editing in noninfected leaves or stems in bamboo without the need for Cas9-expressing transgenic lines, leveraging BaMV's large cargo ability to transport Cas9 proteins.

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引用次数: 0

Centromere diversity and its evolutionary impacts on plant karyotypes and plant reproduction

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-06 DOI: 10.1111/nph.20376

Stefan Steckenborn, André Marques

Karyotype changes are a formidable evolutionary force by directly impacting cross-incompatibility, gene dosage, genetic linkage, chromosome segregation, and meiotic recombination landscape. These changes often arise spontaneously and are commonly detected within plant lineages, even between closely related accessions. One element that can influence drastic karyotype changes after only one (or few) plant generations is the alteration of the centromere position, number, distribution, or even its strength. Here, we briefly explore how these different centromere configurations can directly result in karyotype rearrangements, impacting plant reproduction and meiotic recombination.

引用次数: 0

Resolving the contrasting leaf hydraulic adaptation of C3 and C4 grasses

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-05 DOI: 10.1111/nph.20341

Alec S. Baird, Samuel H. Taylor, Jessica Pasquet-Kok, Christine Vuong, Yu Zhang, Teera Watcharamongkol, Hervé Cochard, Christine Scoffoni, Erika J. Edwards, Colin P. Osborne, Lawren Sack

<h2> Introduction</h2>The grass family (Poaceae) dominates > 40% of the Earth's terrestrial surface with 12 000 species from 800 genera, including the bulk of all crops (Beer et al., 2010; McSteen & Kellogg, 2022). The photosynthetic diversity of grasses is a major factor in their dominance and in their resilience to climate change (Higgins & Scheiter, 2012). More than 40% of extant grass species have C4 photosynthesis, which evolved > 20 times in grasses (of the > 60 times across angiosperms) and is a model for the repeated emergence of a key innovation (Gowik & Westhoff, 2011; Sage et al., 2011; Grass Phylogeny Working Group II, 2012; Marazzi et al., 2012), and the source of high yield in many crops and for novel varieties in development (Gowik & Westhoff, 2011; Langdale, 2011). C4 photosynthesis maximizes carbon fixation, particularly under hotter, drier conditions or low CO2, by concentrating CO2 at Rubisco in the sheath around the leaf veins, minimizing photorespiratory losses, and enabling reduced stomatal conductance per leaf area (gs) and higher light-saturated photosynthetic rate per leaf area (Aarea) relative to gs, resulting in higher intrinsic water use efficiency (WUEi, that is Aarea : gs) (Supporting Information Table S1) (Sage, 2004). Yet, there has been only a fragmentary understanding of the potential contrasts in leaf hydraulic design underlying the photosynthetic and climate adaptation of C3 and C4 grasses, though previous work on grass leaf hydraulic design has indicated its importance in C3 and C4 grass performance (Ocheltree et al., 2014; Baird et al., 2021; Zhou et al., 2021).Generally, across plants, the leaves are bottlenecks in water transport and impose a major limitation on photosynthetic productivity (Meinzer et al., 1992; Martre et al., 2000; Sack & Holbrook, 2006). We extended the theory for the dependence of leaf gas exchange on leaf hydraulic anatomy and physiology established across diverse C3 angiosperms (Sack & Holbrook, 2006; Brodribb et al., 2007) by hypothesizing a novel general framework for the contrasting adaptation of C3 and C4 grasses (Fig. 1; Table 1). The premise of this theory is that water supply through the integrated leaf system needs to match evaporative demand for leaf water potential (Ψleaf) to be maintained high enough for stomata to open for photosynthetic CO2 assimilation (Sack & Holbrook, 2006). Dur

{"title":"Resolving the contrasting leaf hydraulic adaptation of C3 and C4 grasses","authors":"Alec S. Baird, Samuel H. Taylor, Jessica Pasquet-Kok, Christine Vuong, Yu Zhang, Teera Watcharamongkol, Hervé Cochard, Christine Scoffoni, Erika J. Edwards, Colin P. Osborne, Lawren Sack","doi":"10.1111/nph.20341","DOIUrl":"https://doi.org/10.1111/nph.20341","url":null,"abstract":"<h2> Introduction</h2>\u0000The grass family (Poaceae) dominates > 40% of the Earth's terrestrial surface with 12 000 species from 800 genera, including the bulk of all crops (Beer et al., 2010; McSteen & Kellogg, 2022). The photosynthetic diversity of grasses is a major factor in their dominance and in their resilience to climate change (Higgins & Scheiter, 2012). More than 40% of extant grass species have C4 photosynthesis, which evolved > 20 times in grasses (of the > 60 times across angiosperms) and is a model for the repeated emergence of a key innovation (Gowik & Westhoff, 2011; Sage et al., 2011; Grass Phylogeny Working Group II, 2012; Marazzi et al., 2012), and the source of high yield in many crops and for novel varieties in development (Gowik & Westhoff, 2011; Langdale, 2011). C4 photosynthesis maximizes carbon fixation, particularly under hotter, drier conditions or low CO2, by concentrating CO2 at Rubisco in the sheath around the leaf veins, minimizing photorespiratory losses, and enabling reduced stomatal conductance per leaf area (gs) and higher light-saturated photosynthetic rate per leaf area (Aarea) relative to gs, resulting in higher intrinsic water use efficiency (WUEi, that is Aarea : gs) (Supporting Information Table S1) (Sage, 2004). Yet, there has been only a fragmentary understanding of the potential contrasts in leaf hydraulic design underlying the photosynthetic and climate adaptation of C3 and C4 grasses, though previous work on grass leaf hydraulic design has indicated its importance in C3 and C4 grass performance (Ocheltree et al., 2014; Baird et al., 2021; Zhou et al., 2021).\u0000Generally, across plants, the leaves are bottlenecks in water transport and impose a major limitation on photosynthetic productivity (Meinzer et al., 1992; Martre et al., 2000; Sack & Holbrook, 2006). We extended the theory for the dependence of leaf gas exchange on leaf hydraulic anatomy and physiology established across diverse C3 angiosperms (Sack & Holbrook, 2006; Brodribb et al., 2007) by hypothesizing a novel general framework for the contrasting adaptation of C3 and C4 grasses (Fig. 1; Table 1). The premise of this theory is that water supply through the integrated leaf system needs to match evaporative demand for leaf water potential (Ψleaf) to be maintained high enough for stomata to open for photosynthetic CO2 assimilation (Sack & Holbrook, 2006). Dur","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"78 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

C4 photosynthesis and hydraulics in grasses

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-03 DOI: 10.1111/nph.20284

Haoran Zhou, Erol Akçay, Erika J. Edwards, Che‐Ling Ho, Adam Abdullahi, Yunpu Zheng, Brent R. Helliker

Summary

The anatomical reorganization required for C4 photosynthesis should also impact plant hydraulics. Most C4 plants possess large bundle sheath cells and high vein density, which should also lead to higher leaf capacitance and hydraulic conductance (Kleaf). Paradoxically, the C4 pathway reduces water demand and increases water use efficiency, creating a potential mismatch between supply capacity and demand in C4 plant water relations.

Here, we use phylogenetic analyses, physiological measurements, and models to examine the reorganization of hydraulics in closely related C4 and C3 grasses.

The evolution of C4 disrupts the expected positive correlation between maximal assimilation rate (Amax) and Kleaf, decoupling a canonical relationship between hydraulics and photosynthesis generally observed in vascular plants. Evolutionarily young C4 lineages have higher Kleaf, capacitance, turgor loss point, and lower stomatal conductance than their C3 relatives. By contrast, species from older C4 lineages show decreased Kleaf and capacitance. The decline of Kleaf through the evolution of C4 lineages was likely controlled by the reduction in outside‐xylem hydraulic conductance, for example the reorganization of leaf intercellular airspace.

These results indicate that, over time, C4 plants have evolved to optimize hydraulic investments while maintaining the anatomical requirements for the C4 carbon‐concentrating mechanism.

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引用次数: 0

Do pollinators play a role in shaping the essential amino acids found in nectar?

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-02 DOI: 10.1111/nph.20356

Rachel H. Parkinson, Eileen F. Power, Kieran Walter, Alex E. McDermott-Roberts, Jonathan G. Pattrick, Geraldine A. Wright

<h2> Introduction</h2>Floral nectar is produced by plants to attract animals to flowers for pollination (Nicolson & Thornburg, 2007). Most floral nectar is dominated by the presence of sugars (mainly sucrose, glucose, and fructose), but the second most abundant metabolites are free amino acids (AAs) (Nicolson & Thornburg, 2007). Free AAs are ubiquitous in nectar, and although quantities can vary considerably (Baker & Baker, 1975; Gottsberger et al., 1984; Gardener & Gillman, 2001a; Vandelook et al., 2019), they are present at concentrations (micromolar to millimolar) that are substantially lower than the carbohydrates (Nicolson, 2022).Free AAs in nectar can come from the phloem but can also be produced by the nectary itself (reviewed in Göttlinger & Lohaus, 2024). The concentrations of free AAs in nectar are typically lower than in other plant tissues and may be as much as 100-fold lower than in the nectaries and phloem (Lohaus & Schwerdtfeger, 2014; Bertazzini & Forlani, 2016; Göttlinger & Lohaus, 2024). While the nectar AA profile (relative abundance of the different AAs) may resemble that in the nectaries (Göttlinger & Lohaus, 2022), it often differs from nectary (Göttlinger & Lohaus, 2024) and phloem (Lohaus & Schwerdtfeger, 2014; Bertazzini & Forlani, 2016) composition, suggesting that the nectar AA profile is more than just a simple filtering of phloem constituents. Some modification of nectar AAs can occur postsecretion through factors such as pollen contamination or microbial action (Peay et al., 2012; Bogo et al., 2021), though the nectar AA profile could also be under more direct control by plants and driven by pollinator selection (Tiedge & Lohaus, 2017; Göttlinger et al., 2019).Several authors have shown associations between pollinator groups and nectar AA profile and concentration (Baker & Baker, 1975; Petanidou et al., 2006; Tiedge & Lohaus, 2017; Göttlinger & Lohaus, 2024); however, others have found that AAs are not as important as other nectar components (Göttlinger et al., 2019; Vandelook et al., 2019). One criticism of looking for correlations between nectar AAs and pollinator group is that AA concentrations can vary considerably among individuals within a plant species (Gardener & Gillman, 2001a; Gijbels et al., 2014). However, large-scale studies have found that while concentration varies, the relative abundance of individual AAs is much more consistent within species (Gardener & Gillman, 2001a), suggesting AA profil

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引用次数: 0

Can a plant biologist fix a thermostat?

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-02 DOI: 10.1111/nph.20382

Todd P. Michael

The shift to reductionist biology at the dawn of the genome era yielded a ‘parts list’ of plant genes and a nascent understanding of complex biological processes. Today, with the genomics era in full swing, advances in high-definition genomics enabled precise temporal and spatial analyses of biological systems down to the single-cell level. These insights, coupled with artificial intelligence-driven in silico design, are propelling the development of the first synthetic plants. By integrating reductionist and systems approaches, researchers are not only reimagining plants as sources of food, fiber, and fuel but also as ‘environmental thermostats’ capable of mitigating the impacts of a changing climate.

引用次数: 0

The genomic secrets of invasive plants

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2025-01-02 DOI: 10.1111/nph.20368

Kathryn A. Hodgins, Paul Battlay, Dan G. Bock

Genomics has revolutionised the study of invasive species, allowing evolutionary biologists to dissect mechanisms of invasion in unprecedented detail. Botanical research has played an important role in these advances, driving much of what we currently know about key determinants of invasion success (e.g. hybridisation, whole-genome duplication). Despite this, a comprehensive review of plant invasion genomics has been lacking. Here, we aim to address this gap, highlighting recent discoveries that have helped progress the field. For example, by leveraging genomics in natural and experimental populations, botanical research has confirmed the importance of large-effect standing variation during adaptation in invasive species. Further, genomic investigations of plants are increasingly revealing that large structural variants, as well as genetic changes induced by whole-genome duplication such as genomic redundancy or the breakdown of dosage-sensitive reproductive barriers, can play an important role during adaptive evolution of invaders. However, numerous questions remain, including when chromosomal inversions might help or hinder invasions, whether adaptive gene reuse is common during invasions, and whether epigenetically induced mutations can underpin the adaptive evolution of plasticity in invasive populations. We conclude by highlighting these and other outstanding questions that genomic studies of invasive plants are poised to help answer.

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引用次数: 0

Physcomitrium LATERAL SUPPRESSOR genes promote formative cell divisions to produce germ cell lineages in both male and female gametangia

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2024-12-31 DOI: 10.1111/nph.20372

Yuta Horiuchi, Naoyuki Umakawa, Rina Otani, Yosuke Tamada, Ken Kosetsu, Yuji Hiwatashi, Rena Wakisaka, Saiko Yoshida, Takashi Murata, Mitsuyasu Hasebe, Masaki Ishikawa, Rumiko Kofuji

Summary

The evolution of green plants from aquatic to terrestrial environments is thought to have been facilitated by the acquisition of gametangia, specialized multicellular organs housing gametes. Antheridia and archegonia, responsible for producing and protecting sperm and egg cells, undergo formative cell divisions to produce a cell to differentiate into germ cell lineages and the other cell to give rise to surrounding structures. However, the genes governing this process remain unidentified.

We isolated genes expressed during gametangia development from previously established gene‐trap lines of Physcomitrium patens and characterized their function during gametangia formation.

We identified P. patens LATERAL SUPPRESSOR 1 (PpLAS1) from the gene‐trap library, encoding a GRAS transcription factor. The double‐deletion mutant with its paralog PpLAS2 failed to form inner cells in both gametangia. PpLASs are expressed in cells undergoing formative cell division, and introducing PpLAS1 into the double‐deletion mutant successfully rescued the phenotype.

These findings underscore the pivotal role of PpLASs in regulating formative cell divisions, ensuring the separation of reproductive cell lineages from surrounding cells in antheridia and archegonia. Furthermore, they suggest a link between PpLASs and the evolutionary origin of male and female gametangia in the common ancestor of land plants.

{"title":"Physcomitrium LATERAL SUPPRESSOR genes promote formative cell divisions to produce germ cell lineages in both male and female gametangia","authors":"Yuta Horiuchi, Naoyuki Umakawa, Rina Otani, Yosuke Tamada, Ken Kosetsu, Yuji Hiwatashi, Rena Wakisaka, Saiko Yoshida, Takashi Murata, Mitsuyasu Hasebe, Masaki Ishikawa, Rumiko Kofuji","doi":"10.1111/nph.20372","DOIUrl":"https://doi.org/10.1111/nph.20372","url":null,"abstract":"Summary The evolution of green plants from aquatic to terrestrial environments is thought to have been facilitated by the acquisition of gametangia, specialized multicellular organs housing gametes. Antheridia and archegonia, responsible for producing and protecting sperm and egg cells, undergo formative cell divisions to produce a cell to differentiate into germ cell lineages and the other cell to give rise to surrounding structures. However, the genes governing this process remain unidentified. We isolated genes expressed during gametangia development from previously established gene‐trap lines of Physcomitrium patens and characterized their function during gametangia formation. We identified P. patens LATERAL SUPPRESSOR 1 (PpLAS1) from the gene‐trap library, encoding a GRAS transcription factor. The double‐deletion mutant with its paralog PpLAS2 failed to form inner cells in both gametangia. PpLASs are expressed in cells undergoing formative cell division, and introducing PpLAS1 into the double‐deletion mutant successfully rescued the phenotype. These findings underscore the pivotal role of PpLASs in regulating formative cell divisions, ensuring the separation of reproductive cell lineages from surrounding cells in antheridia and archegonia. Furthermore, they suggest a link between PpLASs and the evolutionary origin of male and female gametangia in the common ancestor of land plants. ","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"1 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A tripartite transcriptional module regulates protoderm specification during embryogenesis in Arabidopsis

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2024-12-28 DOI: 10.1111/nph.20371

Chenchen Wang, Yang Gao, Wen Gong, Thomas Laux, Sha Li, Feng Xiong

Summary

Protoderm formation is a crucial step in early embryo patterning in plants, separating the precursors of the epidermis and the inner tissues. Although key regulators such as ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2) have been identified in the model plant Arabidopsis thaliana, the genetic pathways controlling protoderm specification remain largely unexplored.

Here, we combined genetic, cytological, and molecular approaches to investigate the regulatory mechanisms of protoderm specification in Arabidopsis thaliana.

We report a novel role of the β‐importin KETCH1 in protoderm specification. KETCH1 loss‐of‐function leads to aberrant protoderm cell morphology and absent ATML1 transcription in embryos. We further demonstrate that KETCH1 directly interacts with an RNA Polymerase II (Pol‐II) cofactor JANUS, mediating its nuclear accumulation. Furthermore, JANUS directly interacts with the WUS HOMEOBOX2 (WOX2) protein, which is critical for WOX2‐activated ATML1 expression. Consequently, JANUS, KETCH1, and WOX2 loss‐of‐function results in similar protoderm defects.

Our results identify the tripartite KETCH1/JANUS/WOX2 transcriptional module as a novel regulatory axis in Arabidopsis protoderm specification.

{"title":"A tripartite transcriptional module regulates protoderm specification during embryogenesis in Arabidopsis","authors":"Chenchen Wang, Yang Gao, Wen Gong, Thomas Laux, Sha Li, Feng Xiong","doi":"10.1111/nph.20371","DOIUrl":"https://doi.org/10.1111/nph.20371","url":null,"abstract":"Summary Protoderm formation is a crucial step in early embryo patterning in plants, separating the precursors of the epidermis and the inner tissues. Although key regulators such as ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2) have been identified in the model plant Arabidopsis thaliana, the genetic pathways controlling protoderm specification remain largely unexplored. Here, we combined genetic, cytological, and molecular approaches to investigate the regulatory mechanisms of protoderm specification in Arabidopsis thaliana. We report a novel role of the β‐importin KETCH1 in protoderm specification. KETCH1 loss‐of‐function leads to aberrant protoderm cell morphology and absent ATML1 transcription in embryos. We further demonstrate that KETCH1 directly interacts with an RNA Polymerase II (Pol‐II) cofactor JANUS, mediating its nuclear accumulation. Furthermore, JANUS directly interacts with the WUS HOMEOBOX2 (WOX2) protein, which is critical for WOX2‐activated ATML1 expression. Consequently, JANUS, KETCH1, and WOX2 loss‐of‐function results in similar protoderm defects. Our results identify the tripartite KETCH1/JANUS/WOX2 transcriptional module as a novel regulatory axis in Arabidopsis protoderm specification. ","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"23 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes

IF 9.4 1区生物学 Q1 PLANT SCIENCES

New Phytologist

Pub Date : 2024-12-28 DOI: 10.1111/nph.20357

Haochen Li, Jiale Li, Xinchu Li, Jialin Li, Dan Chen, Yangxin Zhang, Qiaoming Yu, Fan Yang, Yunxiao Liu, Weidong Dai, Yaqiang Sun, Pengmin Li, M. Eric Schranz, Fengwang Ma, Tao Zhao

Summary

The clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs).

In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs.

The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots.

Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC‐related BGCs.

{"title":"Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes","authors":"Haochen Li, Jiale Li, Xinchu Li, Jialin Li, Dan Chen, Yangxin Zhang, Qiaoming Yu, Fan Yang, Yunxiao Liu, Weidong Dai, Yaqiang Sun, Pengmin Li, M. Eric Schranz, Fengwang Ma, Tao Zhao","doi":"10.1111/nph.20357","DOIUrl":"https://doi.org/10.1111/nph.20357","url":null,"abstract":"Summary The clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs). In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs. The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots. Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC‐related BGCs. ","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"25 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142888182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0