Dataset Information

Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in Zea mays L. and Its Response to Heavy Metal Stresses.

ABSTRACT: The ATP-binding cassette (ABC) transporter family is one of the largest eukaryotic protein families. Its members play roles in numerous metabolic processes in plants by releasing energy for substrate transport across membranes through hydrolysis of ATP. Maize belongs to the monocotyledonous plant family, Gramineae, and is one of the most important food crops in the world. We constructed a phylogenetic tree with individual ABC genes from maize, rice, sorghum, Arabidopsis, and poplar. This revealed eight families, each containing ABC genes from both monocotyledonous and dicotyledonous plants, indicating that the amplification events of ABC gene families predate the divergence of plant monocotyledons. To further understand the functions of ABC genes in maize growth and development, we analyzed the expression patterns of maize ABC family genes in eight tissues and organs based on the transcriptome database on the Genevestigator website. We identified 133 ABC genes expressed in most of the eight tissues and organs examined, especially during root and leaf development. Furthermore, transcriptome analysis of ZmABC genes showed that exposure to metallic lead induced differential expression of many maize ABC genes, mainly including ZmABC 012, 013, 015, 031, 040, 043, 065, 078, 080, 085, 088, 102, 107, 111, 130 and 131 genes, etc. These results indicated that ZmABC genes play an important role in the response to heavy metal stress. The comprehensive analysis of this study provides a foundation for further studies into the roles of ABC genes in maize.

SUBMITTER: Guo Z

PROVIDER: S-EPMC8879807 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in <i>Zea mays</i> L. and Its Response to Heavy Metal Stresses.

Guo Zhaolai Z Yuan Xinqi X Li Linyang L Zeng Ming M Yang Jie J Tang Hong H Duan Changqun C

International journal of molecular sciences 20220214 4

The ATP-binding cassette (ABC) transporter family is one of the largest eukaryotic protein families. Its members play roles in numerous metabolic processes in plants by releasing energy for substrate transport across membranes through hydrolysis of ATP. Maize belongs to the monocotyledonous plant family, Gramineae, and is one of the most important food crops in the world. We constructed a phylogenetic tree with individual ABC genes from maize, rice, sorghum, <i>Arabidopsis</i>, and poplar. This ...[more]

PMID: 35216220

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Project description:BackgroundThe recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide analysis of these two gene families has been successfully conducted in some plant species, but no systematic evolutionary analysis is available for the flax genome.ResultsHere we describe the ABC transporter and HMA gene families in flax to provide a comprehensive overview of its evolution and some support towards the functional annotation of its members. The 198 ABC transporter and 12 HMA genes identified in the flax genome were classified into eight ABC transporter and four HMA subfamilies based on their phylogenetic analysis and domains' composition. Nine of these genes, i.e., LuABCC9, LuABCC10, LuABCG58, LuABCG59, LuABCG71, LuABCG72, LuABCG73, LuHMA3, and LuHMA4, were orthologous with the Cd associated genes in Arabidopsis, rice and maize. Ten motifs were identified from all ABC transporter and HMA genes. Also, several motifs were conserved among genes of similar length, but each subfamily each had their own motif structures. Both the ABC transporter and HMA gene families were highly conserved among subfamilies of flax and with those of Arabidopsis. While four types of gene duplication were observed at different frequencies, whole-genome or segmental duplications were the most frequent with 162 genes, followed by 29 dispersed, 14 tandem and 4 proximal duplications, suggesting that segmental duplications contributed the most to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were for the most part lower than one, indicative of a predominant purifying selection. Only five pairs of genes clearly exhibited positive selection with a Ka/Ks ratio greater than one. Gene ontology analyses suggested that most flax ABC transporter and HMA genes had a role in ATP binding, transport, catalytic activity, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diversified expression profiling patterns of the genes and revealed their functional or sub-functional conservation and neo-functionalization.ConclusionCharacterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.

Project description:BackgroundLampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates.ResultsWe conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed.ConclusionsThirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC gene subfamilies in chordates have undergone obvious expansion or contraction. The ABCA subfamily showed the highest gene expansion rate during chordate evolution. The evolution of ABC transporters in lampreys requires further evaluation because the present results are based on a draft genome.

Dataset Information

Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in Zea mays L. and Its Response to Heavy Metal Stresses.

Publications

Genome-Wide Analysis of the ATP-Binding Cassette (ABC) Transporter Family in <i>Zea mays</i> L. and Its Response to Heavy Metal Stresses.

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