Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication

TIP aquaporins in Cyperus esculentus: genome-wide identification, expression profiles, subcellular localizations, and interaction patterns

BACKGROUND

Tonoplast intrinsic proteins (TIPs), which typically mediate water transport across vacuolar membranes, play an essential role in plant growth, development, and stress responses. However, their characterization in tigernut (Cyperus esculentus L.), an oil-bearing tuber plant of the Cyperaceae family, is still in the infancy.

RESULTS

In this study, a first genome-wide characterization of the TIP subfamily was conducted in tigernut, resulting in ten members representing five previously defined phylogenetic groups, i.e., TIP1-5. Although the gene amounts are equal to that present in two model plants Arabidopsis and rice, the group composition and/or evolution pattern were shown to be different. Except for CeTIP1;3 that has no counterpart in both Arabidopsis and rice, complex orthologous relationships of 1:1, 1:2, 1:3, 2:1, and 2:2 were observed. Expansion of the CeTIP subfamily was contributed by whole-genome duplication (WGD), transposed, and dispersed duplications. In contrast to the recent WGD-derivation of CeTIP3;1/-3;2, synteny analyses indicated that TIP4 and - 5 are old WGD repeats of TIP2, appearing sometime before monocot-eudicot divergence. Expression analysis revealed that CeTIP genes exhibit diverse expression profiles and are subjected to developmental and diurnal fluctuation regulation. Moreover, when transiently overexpressed in tobacco leaves, CeTIP1;1 was shown to locate in the vacuolar membrane and function in homo/heteromultimer, whereas CeTIP2;1 is located in the cell membrane and only function in heteromultimer. Interestingly, CeTIP1;1 could mediate the tonoplast-localization of CeTIP2;1 via protein interaction, implying complex regulatory patterns.

CONCLUSIONS

Our findings provide a global view of CeTIP genes, which provide valuable information for further functional analysis and genetic improvement through manipulating key members in tigernut.

Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales

Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae-Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon-intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.

Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species

Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors that play important roles in organ development and stress response. However, the function of LBD genes has not been reported in Euphorbiaceae. In this paper, we used Jatropha curcas as the main study object and added rubber tree (Hevea brasiliensis), cassava (Manihot esculenta Crantz) and castor (Ricinus communis L.) to take a phylogenetic analysis of LBD genes. Of LBD, 33, 58, 54 and 30 members were identified in J. curcas, rubber tree, cassava and castor, respectively. The phylogenetic analysis showed that LBD members of Euphorbiaceae could be classified into two major classes and seven subclasses (Ia-Ie,IIa-IIb), and LBD genes of Euphorbiaceae tended to cluster in the same branch. Further analysis showed that the LBD genes of Euphorbiaceae in the same clade usually had similar protein motifs and gene structures, and tissue expression patterns showed that they also have similar expression profiles. JcLBDs in class Ia and Ie are mainly expressed in male and female flowers, and there are multiple duplication genes with similar expression profiles in these clades. It was speculated that they are likely to play important regulatory roles in flower development. Our study provided a solid foundation for further investigation of the role of LBD genes in the sexual differentiaion of J. curcas.

Genome-wide identification and characterization of aquaporins in mangrove plant Kandelia obovata and its role in response to the intertidal environment

Aquaporins (AQPs) play important roles in plant growth, development and tolerance to environmental stresses. To understand the role of AQPs in the mangrove plant Kandelia obovata, which has the ability to acquire water from seawater, we identified 34 AQPs in the K. obovata genome and analysed their structural features. Phylogenetic analysis revealed that KoAQPs are homologous to AQPs of Populus and Arabidopsis, which are evolutionarily conserved. The key amino acid residues were used to assess water-transport ability. Analysis of cis-acting elements in the promoters indicated that KoAQPs may be stress- and hormone-responsive. Subcellular localization of KoAQPs in yeast showed most KoAQPs function in the membrane system. That transgenic yeast with increased cell volume showed that some KoAQPs have significant water-transport activity, and the substrate sensitivity assay indicates that some KoAQPs can transport H₂ O₂ . The transcriptome data were used to analyze the expression patterns of KoAQPs in different tissues and developing fruits of K. obovata. In addition, real-time quantitative PCR analyses combined transcriptome data showed that KoAQPs have complex responses to environmental factors, including salinity, flooding and cold. Collectively, the transport of water and solutes by KoAQPs contributed to the adaptation of K. obovata to the coastal intertidal environment.

Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae

BACKGROUND

Lipid droplets (LDs) present in land plants serve as an essential energy and carbon reserve for seed germination and seedling development. Oleosins, the most abundant structural proteins of LDs, comprise a small family involved in LD formation, stabilization and degradation. Despite their importance, our knowledge on oleosins is still poor in Euphorbiaceae, a large plant family that contains several important oil-bearing species.

RESULTS

To uncover lineage-specific evolution of oleosin genes in Euphorbiaceae, in this study, we performed a genome-wide identification and comprehensive comparison of the oleosin family in Euphorbiaceae species with available genome sequences, i.e. castor bean (Ricinus communis), physic nut (Jatropha curcas), tung tree (Vernicia fordii), Mercurialis annua, cassava (Manihot esculenta) and rubber tree (Hevea brasiliensis), and a number of five, five, five, five, eight and eight members were found, respectively. Synteny analysis revealed one-to-one collinear relationship of oleosin genes between the former four (i.e. castor bean, physic nut, tung tree and M. annua) as well as latter two species (i.e. cassava and rubber tree), whereas one-to-one and one-to-two collinear relationships were observed between physic nut and cassava, reflecting the occurrence of one recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber tree. The presence of five ortholog groups representing three previously defined clades (i.e. U, SL and SH) dates back at least to the Malpighiales ancestor, because they are also conserved in poplar (Populus trichocarpa), a tree having experienced one Salicaceae-specific recent WGD. As observed in poplar, WGD was shown to be the main driver for the family expansion in both cassava and rubber tree. Nevertheless, same retention patterns of WGD-derived duplicates observed in cassava and rubber tree are somewhat different from that of poplar, though certain homologous fragments are still present in rubber tree. Further transcriptional profiling revealed an apparent seed-predominant expression pattern of oleosin genes in physic nut, castor bean and rubber tree. Moreover, structure and expression divergence of paralogous pairs were also observed in both cassava and rubber tree.

CONCLUSION

Comparative genomics analysis of oleosin genes reported in this study improved our knowledge on lineage-specific family evolution in Euphorbiaceae, which also provides valuable information for further functional analysis and utilization of key members and their promoters.

Genome-wide identification of candidate aquaporins involved in water accumulation of pomegranate outer seed coat

Aquaporins (AQPs) are a class of highly conserved integral membrane proteins that facilitate the uptake and transport of water and other small molecules across cell membranes. However, little is known about AQP genes in pomegranate (Punica granatum L.) and their potential role in water accumulation of the outer seed coat. We identified 38 PgrAQP genes in the pomegranate genome and divided them into five subfamilies based on a comparative analysis. Purifying selection played a role in the evolution of PgrAQP genes and a whole-genome duplication event in Myrtales may have contributed to the expansion of PgrTIP, PgrSIP, and PgrXIP genes. Transcriptome data analysis revealed that the PgrAQP genes exhibited different tissue-specific expression patterns. Among them, the transcript abundance of PgrPIPs were significantly higher than that of other subfamilies. The mRNA transcription levels of PgrPIP1.3, PgrPIP2.8, and PgrSIP1.2 showed a significant linear relationship with water accumulation in seed coats, indicating that PgrPIP1.3/PgrPIP2.8 located in the plasma membrane and PgrSIP1.2 proteins located on the tonoplast may be involved in water accumulation and contribute to the cell expansion of the outer seed coat, which then develops into juicy edible flesh. Overall, our results provided not only information on the characteristics and evolution of PgrAQPs, but also insights on the genetic improvement of outer seed coats.

Genome-wide identification and expression analysis of aquaporin family in Canavalia rosea and their roles in the adaptation to saline-alkaline soils and drought stress

BACKGROUND

Canavalia rosea (Sw.) DC. (bay bean) is an extremophile halophyte that is widely distributed in coastal areas of the tropics and subtropics. Seawater and drought tolerance in this species may be facilitated by aquaporins (AQPs), channel proteins that transport water and small molecules across cell membranes and thereby maintain cellular water homeostasis in the face of abiotic stress. In C. rosea, AQP diversity, protein features, and their biological functions are still largely unknown.

RESULTS

We describe the action of AQPs in C. rosea using evolutionary analyses coupled with promoter and expression analyses. A total of 37 AQPs were identified in the C. rosea genome and classified into five subgroups: 11 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, 11 Nod26-like intrinsic proteins, 4 small and basic intrinsic proteins, and 1 X-intrinsic protein. Analysis of RNA-Seq data and targeted qPCR revealed organ-specific expression of aquaporin genes and the involvement of some AQP members in adaptation of C. rosea to extreme coral reef environments. We also analyzed C. rosea sequences for phylogeny reconstruction, protein modeling, cellular localizations, and promoter analysis. Furthermore, one of PIP1 gene, CrPIP1;5, was identified as functional using a yeast expression system and transgenic overexpression in Arabidopsis.

CONCLUSIONS

Our results indicate that AQPs play an important role in C. rosea responses to saline-alkaline soils and drought stress. These findings not only increase our understanding of the role AQPs play in mediating C. rosea adaptation to extreme environments, but also improve our knowledge of plant aquaporin evolution more generally.

Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae

Light-harvesting chlorophyll a/b-binding (Lhc) proteins comprise a plant-specific superfamily involved in photosynthesis and stress responses. Despite their importance, little is known in papaya (Carica papaya), an economically important tree fruit crop as well as a species close to the model plant arabidopsis (Arabidopsis thaliana). This study reports a first genome-wide analysis of Lhc superfamily genes in papaya, and a total of 28 members that represent four defined families or 26 orthologous groups were identified from the papaya genome. The superfamily number is comparable to 28 or 27 reported in castor (Ricinus communis) and jatropha (Jatropha curcas), respectively, two Euphorbiaceous plants also without any recent whole-genome duplication (WGD), but relatively less than 35, 34, 32, 32, 37, 30 or 32 present in cassava (Manihot esculenta), arabidopsis, A. lyrata, A. halleri, Capsella rubella, C. grandiflora, and Eutrema salsugineum, respectively, representative species having experienced one or two recent WGDs. Local duplication was shown to play a predominant role in gene expansion in papaya, castor, and jatropha, which is only confined to the Lhcb1 group. By contrast, WGD plays a relatively more important role in cassava, arabidopsis, and other Brassicaceous plants. Further comparison of Brassicaceous plants revealed that loss of the SEP6 group in arabidopsis is lineage-specific, occurring sometime after papaya-arabidopsis divergence but before the radiation of Brassicaceous plants. Transcriptional profiling revealed a leaf-preferential expression pattern of most CpLhc superfamily genes and their transcript levels were markedly regulated by three abiotic stresses, i.e., mimicking drought, cold, and high salt. These findings not only facilitate further functional studies in papaya, but also improve our knowledge on lineage-specific evolution of this special gene superfamily in Brassicaceae.

Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis

The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.

Genome-Wide Distribution, Expression and Function Analysis of the U-Box Gene Family in Brassica oleracea L

The plant U-box (PUB) protein family plays an important role in plant growth and development. The U-box gene family has been well studied in Arabidopsis thaliana, Brassica rapa, rice, etc., but there have been no systematic studies in Brassica oleracea. In this study, we performed genome-wide identification and evolutionary analysis of the U-box protein family of B. oleracea. Firstly, based on the Brassica database (BRAD) and the Bolbase database, 99 Brassica oleracea PUB genes were identified and divided into seven groups (I-VII). The BoPUB genes are unevenly distributed on the nine chromosomes of B. oleracea, and there are tandem repeat genes, leading to family expansion from the A. thaliana genome to the B. oleracea genome. The protein interaction network, GO annotation, and KEGG pathway enrichment analysis indicated that the biological processes and specific functions of the BoPUB genes may mainly involve abiotic stress. RNA-seq transcriptome data of different pollination times revealed spatiotemporal expression specificity of the BoPUB genes. The differential expression profile was consistent with the results of RT-qPCR analysis. Additionally, a large number of pollen-specific cis-acting elements were found in promoters of differentially expressed genes (DEG), which verified that these significantly differentially expressed genes after self-pollination (SP) were likely to participate in the self-incompatibility (SI) process, including gene encoding ARC1, a well-known downstream protein of SI in B. oleracea. Our study provides valuable information indicating that the BoPUB genes participates not only in the abiotic stress response, but are also involved in pollination.

Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean

Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important non-food oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD, -C, -B, -E, -F, -N, and -H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha.