Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

Rody, Hugo Vianna Silva; Bombardelli, Renato Gustavo Hoffmann; Creste, Silvana; Camargo, L. E. A.; Sluys, Marie‐Anne Van; Monteiro-Vitorello, Cláudia Barros

doi:10.1186/s12864-019-6207-y

Cited by 26 publications

(24 citation statements)

References 66 publications

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“…We found out clustering of RLKs, RLPs, NBS-encoding and TM-CC genes in some chromosome of the four inbred lines (Table S7), in agreement with classical genetics and analysis from large scale sequencing data in plant genomes 36 . The chr.…”

supporting

confidence: 85%

Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value

Acquadro

Barchi

Portis

et al. 2020

Sci Rep

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Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. in addition to commercial varieties and f 1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('Quadrato') and protruding apex or heart shaped ('cuneo'), elongated ('corno') and smaller sized sub-spherical ('tumaticot'). each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'CM334'). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the Snp/indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (ccS) gene. the large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.

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supporting

confidence: 85%

Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value

Acquadro

Barchi

Portis

et al. 2020

Sci Rep

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“…However, SsADH3a, SsADH3b, SsADH4a, SsADH4f, and SbADH2 were not located in the rearranged chromosomal regions. Rody et al [ 22 ] found that the genes that are located in the non-arranged chromosomal regions between AP85–441 and sorghum may represent conserved sources of disease resistance in sugarcane and sorghum. The disease resistance function of ADH requires further study.…”

Section: Discussionmentioning

confidence: 99%

“…Sugarcane ( Saccharum spp.) accounts for 80% of world sugar production [ 22 ]. Modern sugarcane cultivars are produced by hybridizations between Saccharum officinarum L. (2n = 80, high sugar content) and Saccharum spontaneum L. (2n = 40–128, disease resistance) [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation

Ren

Wang

et al. 2020

BMC Genomics

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Background Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in sugarcane is still unclear. Results In the present study, 151 ADH genes from 17 species including 32 ADH genes in Saccharum spontaneum and 6 ADH genes in modern sugarcane cultivar R570 were identified. Phylogenetic analysis demonstrated two groups of ADH genes and suggested that these genes underwent duplication during angiosperm evolution. Whole-genome duplication (WGD)/segmental and dispersed duplications played critical roles in the expansion of ADH family in S. spontaneum and R570, respectively. ScADH3 was cloned and preferentially expressed in response to cold stress. ScADH3 conferred improved cold tolerance in E. coli cells. Ectopic expression showed that ScADH3 can also enhance cold tolerance in transgenic tobacco. The accumulation of reactive oxygen species (ROS) in leaves of transgenic tobacco was significantly lower than in wild-type tobacco. The transcript levels of ROS-related genes in transgenic tobacco increased significantly. ScADH3 seems to affect cold tolerance by regulating the ROS-related genes to maintain the ROS homeostasis. Conclusions This study depicted the size and composition of the ADH gene family in 17 species, and investigated their evolution pattern. Comparative genomics analysis among the ADH gene families of S. bicolor , R570 and S. spontaneum revealed their close evolutionary relationship. Functional analysis suggested that ScADH3 , which maintained the steady state of ROS by regulating ROS-related genes, was related to cold tolerance. These findings will facilitate research on evolutionary and functional aspects of the ADH genes in sugarcane, especially for the understanding of ScADH3 under cold stress.

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“…The clades 4 and 5 appeared to be sister clades and are composed mainly of NBS-encoding proteins with subclades from all other RGA domains and most especially, from TM-CC domains. Rody et al (2019) also observed that TM-CC sequences in sugarcane form widespread subclades across the phylogenetic tree and showed close relationship with NBS-encoding proteins. The clade 6 is composed predominantly of RLKs and shared close relationship to some other RGAs.…”

Section: Resultsmentioning

confidence: 76%

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Lantican

Cortaga

Manohar

et al. 2020

Preprint

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10Plants have developed mechanisms to recognize pathogen and insect attacks and to 11 activate defense response against them through the action of resistance genes (R genes). 12Hence, R gene analogs (RGAs) have been widely studied and efficiently used for breeding of 13 resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, 14 is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from 15 different varieties were identified and characterized via de novo assembly of raw transcriptome 16 sequences currently available in biological repositories. Using bioinformatics pipelines, a core 17 RGA database of mango with 747 protein models was established and were classified based 18 on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide 19 binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 20 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 21 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like 22 proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein 23 (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly 24 clustered the core RGAs into 6 major clades based on their domain classification, while TM- 25CC formed subclades all across the tree. The phylogenetic results suggest highly divergent 26 functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms 27 race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their 29 expression profiles across different mango varieties were also determined. From the mango 30 RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed 31 targeting these potential markers. To date, this is the most comprehensive analysis of mango 32 RGAs which offer a trove of markers for direct utilization in resistance breeding of mango. 33 34 35 36 Introduction 37 Mango (Mangifera indica L.) is a globally popular fruit crop with economical and 38 agricultural significance, especially in the (sub)tropics where it is largely cultivated. One of the 39 constraints in mango production worldwide include a myriad of insect pests (e.g., oriental fruit 40 fly, mango hopper, cecid fly, etc.) and diseases, (e.g., anthracnose, stem-end rot, scab, etc.) 41 which can affect mango at different life stages thus significantly reducing fruit quality and yield 42 (Bally, 2006). These are major barriers to the export market and can impede international 43 trade as many pests and diseases in mango are important quarantine considerations. 44 Along the course of evolution, plants have generally developed mechanisms to 45 recognize pathogen and insect attacks and to activate defense response against them (Dangl 46 and Jones., 2001; Acevedo et al., 2015). The mole...

show abstract

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

Cited by 26 publications

References 66 publications

Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value

Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value

The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

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