Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize

Rabby, Md. Golam; Hossen, Md. Munnaf; Kamal, Md. Mostafa; Islam, Md. Numan

doi:10.1155/2022/2673748

Cited by 4 publications

(2 citation statements)

References 44 publications

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“…For NtLHT identification, the protein sequences of AtLHTs were retrieved from TAIR 1 ( Rhee et al, 2003 ), the obtained sequences were then used as a query to search putative NtLHT genes from the China tobacco genome database (data not shown). Top hits for putative NtLHT proteins were retained on the basis of high scores (score ≥ 0) and low E -values ( E value ≤ 0.1), the NCBI conserved domain database (CDD) 2 was used to analyze the conserved domain (PF01490) of candidate NtLHT proteins ( Rabby et al, 2022 ). After manually removing the redundant sequences, 23 NtLHT genes were identified and used for further bioinformatics and expression analysis.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis

Gao

Wang

et al. 2022

Front. Plant Sci.

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Amino acids are vital nitrogen (N) sources for plant growth, development, and yield. The uptake and translocation of amino acids are mediated by amino acid transporters (AATs). The AATs family including lysine-histidine transporters (LHTs), amino acid permeases (AAPs), and proline transporters (ProTs) subfamilies have been identified in various plants. However, little is known about these genes in tobacco. In this study, we identified 23 LHT genes, the important members of AATs, in the tobacco genome. The gene structure, phylogenetic tree, transmembrane helices, chromosomal distribution, cis-regulatory elements, and expression profiles of NtLHT genes were systematically analyzed. Phylogenetic analysis divided the 23 NtLHT genes into two conserved subgroups. Expression profiles confirmed that the NtLHT genes were differentially expressed in various tissues, indicating their potential roles in tobacco growth and development. Cis-elements analysis of promoters and expression patterns after stress treatments suggested that NtLHT genes probable participate in abiotic stress responses of tobacco. In addition, Knock out and overexpression of NtLHT22 changed the amino acids homeostasis in the transgenic plants, the contents of amino acids were significantly decreased in NtLHT22 overexpression plants than wild-type. The results from this study provide important information for further studies on the molecular functions of the NtLHT genes.

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Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis

Gao

Wang

et al. 2022

Front. Plant Sci.

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“…We identified four transcripts significantly upregulated in thornless blackberries, shedding lights on their potential roles in thorn development. Lysine histidine transporters are involved in importing amino acids into trichomes and play a role in organic N transfer for pollen production (Rabby et al, 2022). MYB domain protein 16 was also upregulated in thornless blackberries.…”

Section: Candidate Genes In the Thorniness Locus Regionmentioning

confidence: 99%

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (RubusL. subgenusRubusWatson)

Paudel

Peng

Parajuli

et al. 2023

Preprint

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Blackberries (Rubus subgenus Rubus) are a major berry crop consumed globally for being a rich source of anthocyanins and antioxidants, and their unique flavor. However, breeding for fruit improvement in blackberry has been significantly hindered by the scarcity of genomic resources and the genetic complexity of traits. The blackberry genome has been particularly challenging to assemble, largely due to its polyploid nature. We present the first chromosome-scale and haplotype-phased genome assembly for the cultivated primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The tetraploid genome assembly was generated using the Oxford Nanopore Technology (ONT) and Hi-C scaffolding, comprising 919 Mb placed on 27 pseudochromosomes with an N50 of 35.73 Mb. The assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Repetitive sequences constitute 57% of the assembly, with the long terminal repeats (LTR) being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Gene expression analyses identified candidate genes and transcription factors related to thornlessness in blackberries, including MYB16, lysine histidine transporters, PDR1, Caffeoyl-CoA, glycosylphosphatidylinositol-anchored lipid protein transfer 1, DRN, beta-ketoacyl reductase, and homocysteine S-methyltransferase 3. The utility of this genome has been demonstrated in this study by identifying candidate genes related to thornlessness in blackberry. Resequencing of tetraploid blackberry cultivars/selections with different horticultural characteristics revealed genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome will serve as a valuable resource to accelerate genetic analysis and breeding of this important berry crop, enabling the development of improved varieties with enhanced traits.

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Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria

Islam¹,

Suzauddula

Ahamed³

et al. 2022

Arch Microbiol

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Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize

Cited by 4 publications

References 44 publications

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (RubusL. subgenusRubusWatson)

Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria

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