Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize

Cao, Yanhua; Zhao, Xing; Liu, Yajuan; Wang, Yalong; Wu, Wen Bing; Jiang, Yiwei; Liao, Changjian; Xu, Xiaoxun; Shen, Yaou; Long, Hai; Zou, Chaoying; Pan, Guangtang; Lin, Hung-Ching

doi:10.7717/peerj.7877

Cited by 30 publications

(28 citation statements)

References 27 publications

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“…Based on previous reports on Arabidopsis, rice, and maize, several ABC transporter and HMA genes are associated with Cd tolerance, including AtABCC1, AtABCC2, AtABCG36, AtHMA3 and AtHMA4 in Arabidopsis [16,21,29,45], OsABCG31, OsABCG36 and OsHMA2 in rice [20,46], as well as ZmHMA2 and ZmHMA3 in maize [34]. We identified seven ABC transporter genes (LuABCC9-LuABCC10, LuABCG58-LuABCG59, and LuABCG71-LuABCG73), and two HMA genes (LuHMA3-LuHMA4) which were orthologous with the above Cd-related genes (Fig.…”

Section: Annotation and Phylogenetic Analysis Of Abc Transporter And mentioning

confidence: 99%

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

et al. 2020

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Background The 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. Results Here 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. Conclusion Characterization of the ABC transporter and HMA gene families will help in the functional analysis of candidate genes in flax and other crop species.

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Section: Annotation and Phylogenetic Analysis Of Abc Transporter And mentioning

confidence: 99%

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

et al. 2020

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“…For the identi cation of ax Cd associated genes, several ABC transporter and HMA responsive genes were used as a reference. These genes included AtABCC1, AtABCC2, AtABCG36, AtHMA3 and AtHMA4 in Arabidopsis [29,[45][46][47], OsABCG31, OsABCG36 and OsHMA2 in rice [20,48], ZmHMA2 and ZmHMA3 in maize [34]. Nine Cd associated genes were identi ed by performing the BLASTP method using the same criteria as discussed above for ABC and HMA genes.…”

Section: Methodsmentioning

confidence: 99%

“…Based on previous reports on Arabidopsis, rice, and maize, several ABC transporter and HMA genes are associated with Cd tolerance, including AtABCC1, AtABCC2,, AtABCG36, AtHMA3 and AtHMA4 in Arabidopsis [29,[45][46][47] , OsABCG31, OsABCG36 and OsHMA2 in rice [20,48], as well as ZmHMA2 and ZmHMA3 in maize [34]. We identi ed seven ABC transporter genes (LuABCC9-LuABCC10, LuABCG58-LuABCG59, and LuABCG71-LuABCG73), and two HMA genes (LuHMA3-LuHMA4) which were orthologous with the above Cd-related genes ( Figure 1c, g and h).…”

Section: Annotation and Phylogenetic Analysis Of Abc Transporter And mentioning

confidence: 99%

“…Thus, the availability of this recent update of the ax genome (version 2.0) constitutes a genomic resource that allows the identi cation of gene families, evolutionary relationships, and structural analyses. To date, ABC transporter and HMA gene families have been studied in several plant species including Oryza sativa and Arabidopsis thaliana [32], Zea mays [33,34], Brassica rapa [7], Brassica napus [35], Triticum aestivum [36], and Vitis vinifera [37]. A previous report on ABC transporters in ax has been published [38], but classi cation patterns, gene duplications, evolutionary and collinear relationships, structural and correlation analyses of paralogous pairs, and the identi cation of Cd associated genes covered herein were not explored in this prior publication.…”

Section: Page 3/21mentioning

confidence: 99%

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Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)

Khan

You

Datla

et al. 2020

Preprint

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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 subfamilies 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.

show abstract

“…Thus, the availability of this recent update of the flax genome (version 2.0) provides a genomic resource that allows the identification of gene families, evolutionary relationship and structural analyses. To date, ABC transporter and HMA gene families have been studied in several plant species including Oryza sativa and Arabidopsis thaliana [31], Zea mays [32,33], Brassica rapa [7], Brassica napus [34], Triticum aestivum [35], and Vitis vinifera [36], but not in flax. In this study, we hypothesized that either whole genome duplications (WGDs) or tandem events contributed to the expansion of the ABC transporter and HMA gene families in flax.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)

Khan

You

Datla

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Flax (Linum usitatissimum L.) is a self-pollinated crop and diversified into two morphotypes for its stem fibre and seed oil. The availability of the flax reference genome sequence, previously assembled into 15 pseudomolecules, enables the characterization of important gene families. The ABC transporter and HMA gene families are considered important gene families 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 several plant species but no systematic study is available for the flax genome. Results Here we described both 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 domain compositions. 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 and several motifs were conserved for all genes with similar gene length, but different subfamilies had their different motif structures. Both the ABC transporter and HMA families were highly conserved among subfamilies of flax and with 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, suggesting that segmental duplications contributed substantially to the expansion of both gene families in flax. The rates of non-synonymous to synonymous (Ka/Ks) mutations of paired duplicated genes were mostly less 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 functioned in ATP binding, transporter, catalytic, ATPase activity, and metal ion binding. The RNA-Seq analysis of eight different organs demonstrated diverse expression profiling patterns of the genes and revealed their functional or subfunctional conservation and neo-functionalization. Conclusion Characterization of the ABC transporter and HMA genes will help in the functional analysis of candidate genes in flax and other crop species.

show abstract

Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize

Cited by 30 publications

References 27 publications

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)

Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)

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