Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C. scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of C. cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of C. scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50 kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in C. scarabaeoides and C. cajan respectively. RNA editing was observed at 37 sites in both C. scarabaeoides and C. cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genome of clusterbean was generated and compared to some of the previously reported legume chloroplast genomes. The chloroplast genome of clusterbean is 152,530 bp in length, with a quadripartite structure consisting of large single copy (LSC) and small single copy (SSC) of 83,025 bp and 17,879 bp in size, respectively, and a pair of inverted repeats (IRs) of 25,790 bp in size. The chloroplast genome contains 114 unique genes, which includes 78 protein coding genes, 30 tRNAs, 4 rRNAs genes, and 2 pseudogenes. It also harbors a 50 kb inversion, typical of the Leguminosae family. The IR region of the clusterbean chloroplast genome has undergone an expansion, and hence, the whole rps19 gene is included in the IR, as compared to other legume plastid genomes. A total of 220 simple sequence repeats (SSRs) were detected in the clusterbean plastid genome. The analysis of the clusterbean plastid genome will provide useful insights for evolutionary, molecular and genetic engineering studies.

Background: Pigeon pea (Cajanus cajan L.) is the sixth major legume crop widely cultivated in the Indian sub-continent, Africa, and Southeast Asia. Cytoplasmic male-sterility (CMS) is the incompetence of flowering plants to produce viable pollens during anther development. CMS has been extensively utilized for commercial hybrid seeds production in pigeon pea. However, the molecular basis governing CMS in pigeon pea remains unclear and undetermined. In this study transcriptome analysis for exploring differentially expressed genes (DEGs) between cytoplasmic male-sterile line (AKCMS11) and its fertility restorer line (AKPR303) was performed using Illumina paired-end sequencing. Results: A total of 3167 DEGs were identified, of which 1432 were up-regulated and 1390 were down-regulated in AKCMS11 in comparison to AKPR303. By querying, all the 3167 DEGs against TAIR database, 34 pigeon pea homologous genes were identified, few involved in pollen development (EMS1, MS1, ARF17) and encoding MYB and bHLH transcription factors with lower expression in the sterile buds, implying their possible role in pollen sterility. Many of these DEGs implicated in carbon metabolism, tricarboxylic acid cycle (TCA), oxidative phosphorylation and elimination of reactive oxygen species (ROS) showed reduced expression in the AKCMS11 (sterile) buds. Conclusion: The comparative transcriptome findings suggest the potential role of these DEGs in pollen development or abortion, pointing towards their involvement in cytoplasmic male-sterility in pigeon pea. The candidate DEGs identified in this investigation will be highly significant for further research, as they could lend a comprehensive basis in unravelling the molecular mechanism governing CMS in pigeon pea.

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Clusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as Guar is a widely 14 cultivated dryland legume of Western India and parts of Africa. Apart from being a vegetable 15 crop, it is also an abundant source of a natural hetero-polysaccharide called guar gum or 16 galactomannan which is widely used in cosmetics, pharmaceuticals, food processing, shale gas 17 drilling etc. Here, for the first time we are reporting a chromosome-scale reference genome 18 assembly of clusterbean, from a high galactomannan containing popular guar cultivar, RGC-936, 19 by combining sequenced reads from Illumina, 10x Chromium and Oxford Nanopore 20 technologies. The initial assembly of 1580 scaffolds with an N50 value of 7.12 Mbp was 21 generated. Then, the final genome assembly was obtained by anchoring these scaffolds to a high 22 density SNP map. Finally, a genome assembly of 550.31 Mbp was obtained in 7 23 pseudomolecules corresponding to 7 chromosomes with a very high N50 of 78.27 Mbp. We 24 finally predicted 34,680 protein-coding genes in the guar genome. The high-quality 25 chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular 26 basis of galactomannan biosynthesis and aid in genomics-assisted breeding of superior cultivars.27 28 Introduction:29 Clusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as guar 1 is a member of 30 Leguminosae family. The common name clusterbean is attributed to its pods which appear in 31 clusters. Previous reports suggest that guar originated in Africa and later spread to the entire 32 South Asian region. In India and Pakistan, clusterbean is cultivated since ancient times for its 33 tender pods which are used as fresh vegetable and the remaining plant serves as fodder 2 . 34Clusterbean is a climate-resilient annual legume and a high potential alternative crop in the 35 marginal lands of arid and semi-arid regions 3 . The genus Cyamopsis includes four species i.e., 36 one cultivated C. tetragonoloba (L.) Taub., two wild relatives C. serrata Schinz, and C. 37senegalensis Guill&Perr, and C. dentate Tarre, and an interspecies hybrid of C. serrata and C.38 senegalensis 4. A mature clusterbean seed is composed of three parts: germ (43-47%), endosperm 39 (35-42%), and seed coat (14-17%). About 80-90% of the endosperm is composed of highly 40 viscous water-soluble hetero-polysaccharide called gaur gum (or) galactomannan, having a 1:2 41 ratio of galactose to mannose 5 . Guar gum is extensively utilized as natural thickener, emulsifier 42 and stabilizers in the food, textile, paper, petroleum and pharmaceutical industry with increasing 43 global demand 6-9 . With the annual production of ~1-1.25 million tons of clusterbean seeds, India 44 accounts for 80% of the global production, with several other countries,

Cyamopsis tetragonoloba (L) endosperm predominantly contains guar gum a polysaccharide, which has tremendous industrial applications in food, textile, paper, oil drilling and water treatment. In order to understand the genes controlling galactomannan biosynthesis, mRNA was isolated from seeds collected at different developmental stages; young pods, mature pods and young leaf from two guar varieties, HG365 and HG870 and subjected to Illumina sequencing. De novo assembly of fourteen individual read files from two varieties of guar representing seven developmental stages gave a total of 1,13,607 contigs with an N50 of 1,244 bases. Annotation of assemblies with GO mapping revealed three levels of distribution, namely, Biological Processes, Molecular Functions and Cellular Components. GO studies identified major genes involved in galactomannan biosynthesis: Cellulose synthase D1 (CS D1) and GAUT-like gene families. Among the polysaccharide biosynthetic process (GO:0000271) genes the transcript abundance for CS was found to be predominantly more in leaf samples, whereas, the transcript abundance for GAUT-like steadily increased from 65% to 90% and above from stage1 to stage5 indicating accumulation of galactomannan in developing seeds; and validated by qRT-PCR analysis. Galactomannan quantification by HPLC showed HG365 (12.98–20.66%) and HG870 (7.035–41.2%) gradually increasing from stage1 to stage 5 (10–50 DAA) and highest accumulation occurred in mature and dry seeds with 3.8 to 7.1 fold increase, respectively. This is the first report of transcriptome sequencing and complete profiling of guar seeds at different developmental stages, young pods, mature pods and young leaf material from two commercially important Indian varieties and elucidation of galactomannan biosynthesis pathway. It is envisaged that the data presented herein will be very useful for improvement of guar through biotechnological interventions in future.

2023), Transcriptome profiling of two contrasting pigeon pea (Cajanus cajan) genotypes in response to waterlogging stress.

Pigeonpea (Cajanus cajan (L) Millsp) is a short-day plant in which the owering is highly sensitive to photoperiod. A better understanding of the genes modulating photoresponse and owering time is critical to developing photoperiod insensitive pigeonpea cultivars for cultivation across the seasons. We identi ed 33 CCT family genes (CcCCT1-CcCCT33) in C. cajan and localized them on 10 chromosomes and nine genomic scaffolds. The structural analysis of CCT family genes revealed a considerable variation in length and distribution of exons and introns. Based on the type of domain(s), we classi ed the CCT family genes into CCT motif family (CMF) type, CONSTANS like (COL) type, Pseudo-response Regulator (PRR) type, and GATA and ti containing CCT (GTCC) type. The CCT family genes of C. cajan exhibited an extensive orthologous relationship with the CCT family genes of other legume species. We also observed signi cant sharing of CCT family genes among the legume species. Glycine max exhibited the maximum sharing of CCT family genes with C. cajan. The analysis of CCT family proteins-based phylogenic relationships revealed a general congruence with the legumes' taxonomic relationships. The expression analysis of CCT family genes of pigeonpea demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS (CO) in ICP20338. In contrast, only CcCCT23 is active in MAL3, explaining the differential response of ICP20338 and MAL3 to photoperiod. The chromosomes of C. cajan contain a variable number of CCT family genes. A majority of these genes are localized in the centromeric regions. The COL type CCT genes are structurally highly diverse and contain a variable number of B-box domains. The CCT family genes of different legume species exhibit all three kinds of relationships: one-to-one, many-to-one, and many-tomany types. The photoperiod insensitive cultivar ICP20338 contains CcCCT4 and CcCCT23, while the photoperiod sensitive cultivar MAL3 contains only CcCCT23 as active CONSTANS (CO), which may be the plausible reason for their differential photoperiod response.