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Motivation Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery. Results In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties. Supplementary information Supplementary data are available at Bioinformatics online.

The effector proteins expressed by plant pathogens are one of the essential components of the host-pathogen interaction. Despite being important, most of the effector proteins remain unexplored due to the lack of conserved features and huge diversity in their primary sequence. In the present study, extensive secretome analysis was performed in sixteen major plant fungal pathogens to find the conserved features in the candidate secretory effector proteins (CSEPs) using homology and ab initio modeling approaches. Interestingly, a variable number of plant kiwellin proteins fold like secretory proteins were found in all the major rust fungal pathogens. Many of them are predicted as potential effector proteins. For instance, 26 out of 35 Kiwellin like proteins identified in Puccinia striiformis race 104E 137A were predicted as potential effector proteins. In addition, a kiwellin predicted effector gene, Pst_13960, from the Indian Puccinia striiformis race Yr9 was characterized using overexpression, localization, and deletion studies in Nicotiana benthamiana. The Pst_13960 suppressed the BAX-induced cell death and localized in the chloroplast. Furthermore, the expression of the kiwellin matching region (Pst_13960_kiwi) alone suppressed the BAX-induced cell death in N. benthamiana despite the change of location to the cytoplasm and nucleus, suggesting the novel function of the kiwellin fold in rust fungi. Further analysis of these proteins predicted these candidates to contain N-terminal Intrinsically disordered regions (IDRs) putatively associated with chloroplast translocation as deletion of region abolished the chloroplast localization of Pstr_13960. Overall, the current study reports the presence of kiwellin like proteins in rust fungi that act as a novel effector in plants.Author SummaryRust fungi are one of the most devastating plants infecting pathogens. These pathogens secrete several distinct proteins like effector proteins that help the pathogens in the establishment of infection by suppressing cell death induced by the plants. Despite being important, these effector proteins remain unexplored due to the lack of conserved features. Currently, different methods are being used to characterize them however, could not describe their specific function fully due to a lack of knowledge of the functional domain. Recent advancement in effector protein tertiary structure characterization using NMR (Nuclear magnetic resonance) and X-ray crystallography has been very helpful in identifying the conserved structural features defining functionality. However, these techniques are quite complicated and may take a lot of time and labor. On the other hand, the computational approaches for structural prediction of the effectors may help to identify known folds or domains with few efforts but at a significant level. Therefore, such computational approaches can be efficiently implemented in the preliminary screening of the candidates. In the present study using the computational structure prediction method, we were able to find several conserved novel kiwellin folds containing effectors, in different rust fungi. We characterized one of the candidates and it showed interference with artificially induced cell death in plants. This study highlights the novel function of the kiwellin like effector proteins of the rust fungi that are already identified to play a role in host defense against plant pathogens.

With the progress of sequencing technology coupled with in silico approaches, disclosure of long non-coding RNA (lncRNAs) from RNAseq data has become easy and reliable. Till today, no methodical investigation of lncRNAs and their regulatory roles in tea have been studied. In this study, using 170 RNAseq data (˜7157 million reads) of 11 harvestable tissues, 33,400 putative high certainty lncRNAs were discovered, among which 99.76% were found to be putative novel lncRNAs. The expression analysis of lncRNAs from 53 RNAseq data of 7 tissues (axillary bud, a bud and a leaf, a bud and 2 leaves, apical bud and 2 leaves, 2nd leaf, 4th leaf, and 6th leaf) demonstrated their tissue-specific expression. Further, around 1,654 lncRNAs were found to be endogenous target mimics of miRNAs that interacted with 698 mRNAs of tea genome. Based on their target i.e. coding-gene partners by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway showed that 378 lncRNAs are involved in major aroma formation pathway of tea. Present study also provides valuable information to uncover the various molecular functions of lncRNAs that regulate aroma formation of tea.

Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.

Tea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

The jumonji (JMJ)-C domain containing proteins belong to histone demethylases family with the ability to demethylate the tri-methylated histone residues. They act as chromatin regulators to regulate many physiological functions in plants. The present study deals with the characterization of JMJ-C gene family members in wild as well as cultivated rice species and their expression analysis in salt tolerant rice genotype, FL478. The genome wide study identified 151 members belonging to JMJ-C gene family in 11 different Oryza species. We also studied their structure, genomic location, gene duplication events, phylogenetic relationship, in silico expression analysis and identified cis elements in their promoters. We also found a few JMJ-C gene family members in rice which underwent duplication before the whole genome duplication event of the rice. The qRT-PCR based expression profiling revealed that out of the total 15 rice JMJ-C members, two were highly expressed in the flag leaf stage of FL478 under salt treatment. These two candidate JMJ-C members were also found to render salinity tolerance when over-expressed in yeast cells. Thus, the present study helps in further structural as well as functional characterization of JMJ-C genes under salinity stress in Oryza species.

NBS-encoding genes play a critical role in the plant defense system. Wild relatives of crop plants are rich reservoirs of plant defense genes. Here, we performed a stringent genome-wide identification of NBS-encoding genes in three cultivated and eight wild Oryza species, representing three different genomes (AA, BB, and FF) from four continents. A total of 2688 NBS-encoding genes were identified from 11 Oryza genomes. All the three progenitor species of cultivated rice, namely O. barthii, O. rufipogon, and O. nivara, were the richest reservoir of NBS-encoding genes (214, 313, and 307 respectively). Interestingly, the two Asian cultivated species showed a contrasting pattern in the number of NBS-encoding genes. While indica subspecies maintained nearly equal number of NBS genes as its progenitor (309 and 313), the japonica subspecies had retained only two third in the course of evolution (213 and 307). Other major sources for NBS-encoding genes could be (i) O. longistaminata since it had the highest proportion of NBS-encoding genes and (ii) O. glumaepatula as it clustered distinctly away from the rest of the AA genome species. The present study thus revealed that NBS-encoding genes can be exploited from the primary gene pool for disease resistance breeding in rice.

Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61–0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/

Camellia assamica L. (O). Kuntze. var. TV-1 from Assam, India is one of the most important tea cultivar of Indian Tea Industry which botanically belongs to Assam type and has distinct morphological as well as chemical constituent in leaf than China type of tea. We here present the first draft genome sequence of TV-1, assembled in 2.93 Gb size comprising of 14,824 scaffolds and covering 97.66% of the predicted genome size (3.0 Gb) as determined by flow cytometry. The N50 value, longest and average contig size for this draft genome was found to be as 538.96 Kb, 3.64 Mb and 197.99 Kb, respectively. There were 495,747 SSRs (Di- to Hexa-mers) in the genome and the repeat contents accounted for 71.87% of the genome. About 94.40% genome completeness was predicted with BUSCO, maximum among the published and reported tea genomes. The clustering of the assembled genome with Hi-C data resulted in 15 clusters ranging from the size of 631.46 Mb to 14.39 Mb and accounting 99.32% of assembled genome. This data will act as the starting point for unravelling the important genes and differentiating Indian tea from other commercially available tea varieties.

The NCBI database has >15 chloroplast (cp) genome sequences available for different Camellia species but none for C. assamica. There is no report of any mitochondrial (mt) genome in the Camellia genus or Theaceae family. With the strong believes that these organelle genomes can play a great tool for taxonomic and phylogenetic analysis , we successfully assembled and analyzed cp and mt genome of C. assamica. We assembled the complete mt genome of C. assamica in a single circular contig of 707,441 bp length comprising of a total of 66 annotated genes, including 35 protein-coding genes, 29 tRNAs and two rRNAs. The first ever cp genome of C. assamica resulted in a circular contig of 157,353 bp length with a typical quadripartite structure. Phylogenetic analysis based on these organelle genomes showed that C. assamica was closely related to C. sinensis and C. leptophylla . It also supports Caryophyllales as Superasterids.

Oryza coarctata (KKLL; 2n = 4x = 48, 665 Mb) also known as Porteresia coarctata is an extreme halophyte species of genus Oryza. Using Illumina and Nanopore reads, we achieved the assembled genome size of 569.9 Mb, accounting 85.69% of the estimated genome size with N50 of 1.85 Mb and 19.89% repetitive region. We also found 230,968 simple sequence repeats (SSRs) and 5,512 non-coding RNAs (ncRNAs). The functional annotation of predicted 33,627 protein-coding genes and 4,916 transcription factors revealed that high salinity adaptation of this species is due to the exclusive or excessive presence of stress-specific genes as compared to rice. We have identified 8 homologs to salt-tolerant SOS1 genes, one of the three main components of salt overly sensitive (SOS) signal pathway. On the other hand, the phylogenetic analysis of the assembled chloroplast (134.75 kb) and mitochondrial genome (491.06 kb) favours the conservative nature of these organelle genomes within Oryza taxon.

Climate change-induced abiotic stresses are major limitations to crop growth and development. Among the various stresses, soil salinity is a major concern, as percentage of soil salinization has increased due to the increase in the level of ocean water and increase in irrigated area. Biotechnology and precision breeding techniques can be efficiently utilized to cope up with this abiotic stress. However, the prerequisite of the utilization of such technique requires suitable genetic resources consisting salt stress responsive genes can be deployed against this stress. Wild relatives are known to be the excellent source of such favorable alleles. Oryza coarctata is the only wild halophyte in the genus Oryza, which can withstand salinity up to 40 ds/m due to presence of distinct anatomical, morphological and physiological characteristics. Several metabolites and their genes had been elucidated in this plant for their role in imparting salt tolerance. In this chapter, we have compiled all the relevant information to understand the mechanism for salinity and waterlogging tolerance of this species. Additionally, we also identified the research gaps that need to be addressed to harness the beneficial genes/QTLs from this important halophyte.

Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ) unigenes. We annotated 79% unigenes against Plant Genes from the National Center for Biotechnology Information (NCBI), Swiss-Prot, Pfam, gene ontology (GO) and KEGG databases. Among the annotated unigenes, 30,020 were assigned with 116,964 GO terms, 9984 with EC and 6111 with 137 KEGG pathways. At different fragments per kilobase of transcript per millions fragments sequenced (FPKM) levels, genes were found expressed higher in flower tissue followed by shoot and leaf. Additionally, we identified 8687 potential simple sequence repeats (SSRs) with an average frequency of one SSR per 8.75 kb. A total of 28 amplified SSRs in 21 clusterbean genotypes resulted in polymorphism in 13 markers with average polymorphic information content (PIC) of 0.21. We also constructed a database named ‘ClustergeneDB’ for easy retrieval of unigenes and the microsatellite markers. The tissue specific genes identified and the molecular marker resources developed in this study is expected to aid in genetic improvement of clusterbean for its end use.

Leaf or brown rust caused by Puccinia triticina (Pt) is one of the most important diseases of wheat. Among the rusts, it is the most ubiquitous in all the wheatgrowing regions and causes considerable yield loss. Microsatellite marker-based genotyping and virulence- based phenotyping of 48 pathotypes of Pt was performed. The pathotypes exhibit low virulence frequencies for Indian leaf rust differentials Lr24, Lr9, Lr10, Lr19, Lr28 and Lr9 . Using avirulence/virulence formula six major clusters of pathotypes were observed, revealing high degree of phenotypic variation. Molecular analysis performed using SSR markers showed high genetic diversity among the pathotypes, and grouped them in seven major clusters. The percentage of polymorphic loci ranged from 17.95 to 84.62, Nei's gene diversity from 0.07 to 0.32 and Shannon's information index from 0.11 to 0.47. Analysis of molecular variance revealed significantly high genetic variation within Pt population. Mantel's Z test proved low positive correlation (r = 0.28) between virulence and molecular diversity, suggesting independent nature of the duo. These findings offer valuable information for framing suitable disease management strategies through appropriate region-specific gene deployment and improve the understanding of the population biology and evolution of Pt in the Indian subcontinent.

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine maxandMedicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor,Zea mays, andOryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.