A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance

The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.

A high-quality genome assembly of Morinda officinalis,a famous native southern herb in the Lingnan region of southern China

Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China.Its dried roots(called bajitian in traditional Chinese medicine)are broadly used to treat various diseases,such as impotence and rheumatism.Here,we report a high-quality chromosome-scale genome assembly of M.officinalis using Nanopore single-molecule sequencing and Hi-C technology.The assembled genome size was 484.85Mb with a scaffold N50 of 40.97 Mb,and 90.77%of the assembled sequences were anchored on eleven pseudochromosomes.The genome includes 27,698 protein-coding genes,and most of the assemblies are repetitive sequences.Genome evolution analysis revealed that M.officinalis underwent core eudicotγgenome triplication events but no recent whole-genome duplication(WGD).Likewise,comparative genomic analysis showed no large-scale structural variation after species divergence between M.officinalis and Coffea canephora.Moreover,gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in M.officinalis.Furthermore,we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones,iridoids and polysaccharides.In addition,we also found that the DHQS,GGPPS,TPS-Clin,TPS04,sacA,and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in M.officinalis.This study provides a valuable resource for understanding M.officinalis genome evolution and active component biosynthesis.This work will facilitate genetic improvement and molecular breeding of this commercially important plant.

Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane(Saccharum spp.) clonal F_(1) population

The ratoon stunting disease (RSD) of sugarcane,caused by the bacterium Leifsonia xyli subsp.xyli,is one of the major concerns to sugarcane production and breeding programs worldwide.Due to no obvious external symptoms,RSD cannot be easily detected by the growers,hence has reduced the world’s sugarcane production significantly.This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection.A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay.Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population,linkage map construction and QTL analysis were conducted based on clonal F_1 and F_2 mapping population types with GACD V.1.2 and Ici Mapping V.3.3,respectively.A total of 23 QTL associated with RSD resistance were identified,which explained 6%to13%of the phenotypic variation with the two types of software.A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes),sugarcane R570 genome (20 genes),and S.spontaneum genome (18 genes),respectively.Compared with Ici Mapping V.3.3,GACD V.1.2 identified more major (6 vs.3) and stable QTL (2vs.0),and more disease resistance genes (51 vs.31),indicating GACD V.1.2 (clonal F_1 mapping type) is most likely to be more efficient than Ici Mapping (F_2 mapping type) for QTL analysis of a sefling population or clonal F_1 population in clonal species.The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease.

Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

Erianthus arundinaceus is a wild relative of sugarcane(Saccharum officinarum L.)with many desirable agronomic traits for sugarcane genetic improvement.However,limited knowledge of the complex genome of hexaploid E.arundinaceus has impeded the development of required molecular tools.Dissecting complex genomes into single chromosomes can simplify analyses.The flow-cytometric sorting of a single chromosome of E.arundinaceus in a Saccharum-Erianthus introgression line is reported.A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size.A total of 218,000 E.arundinaceus chromosome 1(EaC1)were sorted to>97%purity and amplified DNA was sequenced using Illumina and Pac Bio technologies.The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb.A total of 56.69 Mb repeat sequences were predicted,accounting for 79.1%of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59%of the chromosome.Of these genes,1877(70.9%)genes were functionally annotated.The phylogenetic relationship of E.arundinaceus with other species using the chromosome1 sequence revealed that E.arundinaceus was distantly related to Oryza sativa and Zea mays,followed by Sorghum bicolor,and was closely related to S.spontaneum and Saccharum spp.hybrids.This study provides the first insights into the characteristics of EaC1,and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

Manganese toxicity-induced chlorosis in sugarcane seedlings involves inhibition of chlorophyll biosynthesis

Manganese(Mn)toxicity-induced leaf chlorosis limits crop production in acidic soils,but its underlying mechanisms remain unknown.The effects of excessive Mn on chlorophyll(Chl)biosynthesis in sugarcane(Saccharum officinarum L.)leaves were investigated.Under Mn treatment,Chl concentration decreased with Mn accumulation and chlorosis appeared in expanding leaves.Before that,levels of the initial Chl precursor 5-aminolevulinic acid(ALA)and its downstream intermediates decreased,whereas magnesium-protoporphyrin IX monomethyl ester(MgPME)accumulated.Overaccumulation of Mn in leaves downregulated the ALA biosynthetic gene GluTR(encoding glutamyl-tRNA reductase)and MgPME conversion gene MgPMEC(encoding MgPME cyclase),upregulated the ALA biosynthesis inhibitor FLU(encoding FLUORESCENT),but had no significant effect on the expression of other Chl biosynthetic genes.The above Mn-induced changes of Chl precursors and expression of corresponding genes commenced before the Chl decline and leaf chlorosis,and were reversed by ALA supplementation.Thus,excessive Mn-induced chlorosis in sugarcane is mediated by a Chl-biosynthesis disorder resulting from the inhibition of ALA synthesis and MgPME conversion.

Correlativity between blood measures related to blood stasis blocking collaterals and gene expression of angiotensin-converting enzyme of renal cortex in diabetic rats and effect of stasis removing and collaterals dredging

OBJECTIVE: To investigate the correlativity between the changes of blood measures related to blood stasis blocking collaterals and gene expression levels of angiotensin-converting enzyme(ACE)and ACE2 ofrenal cortex in diabetic rats with stasis blocking collaterals syndrome, as well as the effectof stasis removing and collaterals dredging.METHODS: Male Sprague-Dawley rats were divided randomly into normal control group(C group),high-carbohydrate-fat control group(H group) and streptozotocin(STZ)-injecting group. The diabeticrats were induced from rats in the STZ-injecting groupby high-carbohydrate-fat diet combined with STZ intraperitoneal injection, with sustained high-carbohydrate-fat diet fed afterwards, and were further divided into model group(M group)and Chinese medicine of stasis removing and collaterals dredging group(Z group). Rats in the Z group were fed with stasis-removing-and-collaterals-dredging herbal granule suspension intragastrically daily for 16 weeks, while drinking water of corresponding volume was administrated to the rats in other groups. At the end of the 16 th week after successful establishment of models, the ultrastructures of glomeruli in different groups were detected by a transmission electron microscopy; and blood measures related to blood stasis blocking collaterals, including lipid profile and blood viscosity measures, were tested, as well as the relative gene expressions of ACE and ACE2.RESULTS: Changes in ultrastructures of glomeruli in the M group were characterized by lack of clarity in structure and occasional thickening of glomerular basement membrane and extensive fusion in foot processes. The correlation analysis showed that there were positive correlations between lipid profile, blood viscosity, and the ACE mRNA expression levels in the M group(P<0.05), except for cholesterol. And except for triglyceride, the blood measures were in negative correlation with the ACE2 mRNA expression levels in the M group(P<0.05).Compared with the C and H groups, the lipid profile, plasma viscosity and blood viscosity were significantly higher(P<0.01). All the above-mentioned measures were significantly improved in the Z group rats(P<0.05). ACE mRNA expression was significantly higher in the M group thanin the C group(P<0.05). ACE2 mRNA level was significantly lower in the M group than in the C and H groups(P<0.01)and its levelin the Z group was higher than that in the M group(P<0.01).CONCLUSION: Blood measuresrelated to blood stasis blocking collaterals had positive linear correlations with ACE mRNAexpression and negative linear correlations with ACE2 mRNA expression in the M group. Chinese recipe of stasis removing and collaterals dredging could play a renal protecting role for diabetic rats by reducing lipid profile and blood viscosity, down-regulating ACE mRNA expression and up-regulating ACE2 mRNA expression.