Technology-enabled great leap in deciphering plant genomes

Xie, Lingjuan; Gong, Xiaojiao; Yang, Kun; Huang, Yujie; Zhang, Shiyu; Shen, Leti; Sun, Yanqing; Wu, Dongya; Ye, Chuyu; Zhu, Qian-Hao; Fan, Longjiang

doi:10.1038/s41477-024-01655-6

Cited by 8 publications

(5 citation statements)

References 173 publications

(44 reference statements)

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“…The article by Xie et al ( 2024 ) was published where they present the N3 database on plant genome sequence efforts: http://ibi.zju.edu.cn/N3database/index.php .…”

Section: Note Added In Proofmentioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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Main conclusion In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Abstract Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

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“…The article by Xie et al ( 2024 ) was published where they present the N3 database on plant genome sequence efforts: http://ibi.zju.edu.cn/N3database/index.php .…”

Section: Note Added In Proofmentioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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“…Other commercially important species such as guava (Psidium guajava L.) (Feng et al 2021) and clove (Syzygium aromaticum L.) (Ouadi et al 2022) have also had their genomes published. Rapid technological advances in long-read sequencing present new opportunities for plant genomics (Dumschott et al 2020;Xie et al 2024). Notably, the chromosome-level gap-free T2T genome assembly of Rhodomytus tormentosa (Aiton) Hassk.…”

Section: Genomic Resources For Myrtle Rustmentioning

confidence: 99%

Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data

Chen,

Jones,

Lu-Irving

et al. 2024

Preprint

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Technological advances have propelled DNA sequencing of non-model organisms, making sequencing more accessible and cost effective, which has also increased the availability of raw data in public repositories. However, contamination is a significant concern, and the use and reuse of sequencing data requires quality control and curation. A reference genome for the Australian native rainforest treeRhodamnia argenteaBenth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp assembly anchored to 11 chromosomes (2n= 22). TheR. argenteagenome will inform conservation efforts for Myrtaceae species threatened by the global spread of the fungal disease myrtle rust. We observed contamination in the sequencing data and further investigation revealed an arthropod source. Here, we demonstrate the feasibility of assembling a high-quality gapless telomere-to-telomere mite genome using contaminated host plant sequencing data. The mite exhibits genome streamlining and has a 35 Mbp genome (68.6% BUSCO completeness) on two chromosomes, capped with a novel TTTGG telomere sequence. Phylogenomic analysis suggests that it is a previously unsequenced eriophyoid mite. Despite its unknown identity, this complete nuclear genome provides a valuable resource to investigate invertebrate genome reduction. This study emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of two species, including a tree that faces substantial conservation challenges, contributing to broader biodiversity initiatives.

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“…Complete genome sequencing of plant species is rapidly progressing; 3517 genomes were sequenced from 1575 plant species from 2000 to 2024 [ 14 ]. This helped to discover many sequences encoding nitrate transporters of different families including NRT2.…”

Section: Introductionmentioning

confidence: 99%

“…AtNRT2.7 is specifically expressed in seeds; it is the only NRT2 transporter located in tonoplast for loading NO 3 − into vacuoles [13]. Complete genome sequencing of plant species is rapidly progressing; 3517 genomes were sequenced from 1575 plant species from 2000 to 2024 [14]. This helped to discover many sequences encoding nitrate transporters of different families including NRT2.…”

Section: Introductionmentioning

confidence: 99%

Novel Proteins of the High-Affinity Nitrate Transporter Family NRT2, SaNRT2.1 and SaNRT2.5, from the Euhalophyte Suaeda altissima: Molecular Cloning and Expression Analysis

Khramov,

Rostovtseva,

Matalin

et al. 2024

IJMS

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Two genes of nitrate transporters SaNRT2.1 and SaNRT2.5, putative orthologs of high-affinity nitrate transporter genes AtNRT2.1 and AtNRT2.5 from Arabidopsis thaliana, were cloned from the euhalophyte Suaeda altissima. Phylogenetic bioinformatic analysis demonstrated that the proteins SaNRT2.1 and SaNRT2.5 exhibited higher levels of homology to the corresponding proteins from the plants of family Amaranthaceae; the similarity of amino acid sequences between proteins SaNRT2.1 and SaNRT2.5 was lower (54%). Both SaNRT2.1 and SaNRT2.5 are integral membrane proteins forming 12 transmembrane helices as predicted by topological modeling. An attempt to demonstrate nitrate transporting activity of SaNRT2.1 or SaNRT2.5 by heterologous expression of the genes in the yeast Hansenula (Ogataea) polymorpha mutant strain Δynt1 lacking the only yeast nitrate transporter was not successful. The expression patterns of SaNRT2.1 and SaNRT2.5 were studied in S. altissima plants that were grown in hydroponics under either low (0.5 mM) or high (15 mM) nitrate and salinity from 0 to 750 mM NaCl. The growth of the plants was strongly inhibited by low nitrogen supply while stimulated by NaCl; it peaked at 250 mM NaCl for high nitrate and at 500 mM NaCl for low nitrate. Under low nitrate supply, nitrate contents in S. altissima roots, leaves and stems were reduced but increased in leaves and stems as salinity in the medium increased. Potassium contents remained stable under salinity treatment from 250 to 750 mM NaCl. Quantitative real-time PCR demonstrated that without salinity, SaNRT2.1 was expressed in all organs, its expression was not influenced by nitrate supply, while SaNRT2.5 was expressed exclusively in roots—its expression rose about 10-fold under low nitrate. Salinity increased expression of both SaNRT2.1 and SaNRT2.5 under low nitrate. SaNRT2.1 peaked in roots at 500 mM NaCl with 15-fold increase; SaNRT2.5 peaked in roots at 500 mM NaCl with 150-fold increase. It is suggested that SaNRT2.5 ensures effective nitrate uptake by roots and functions as an essential high-affinity nitrate transporter to support growth of adult S. altissima plants under nitrogen deficiency.

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Technology-enabled great leap in deciphering plant genomes

Cited by 8 publications

References 173 publications

Plant genome information facilitates plant functional genomics

Plant genome information facilitates plant functional genomics

Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data

Novel Proteins of the High-Affinity Nitrate Transporter Family NRT2, SaNRT2.1 and SaNRT2.5, from the Euhalophyte Suaeda altissima: Molecular Cloning and Expression Analysis

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