Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis

Kaila, Tanvi; Chaduvla, Pavan K.; Rawal, Hukam C.; Saxena, Swati; Tyagi, Anshika; Mithra, S. V. Amitha; Solanke, Amolkumar U.; Kalia, Pritam; Sharma, Tilak Raj; Singh, Nagendra; Gaikwad, Kishor

doi:10.3390/genes8090212

Cited by 48 publications

(33 citation statements)

References 106 publications

(128 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, prior studies documented a 50-kb inversion that spans the genes rbcL and rps16 in the plastomes of C. cajan and C. scarabaeoides (Kaila et al, 2016) and Cyamopsis tetragonoloba (L.) Taub. (Kaila et al, 2017) in the MP clade. By analyzing additional taxa of the MP clade, we discovered six new inversions in three tribes (Desmodieae, Milletieae, and Phaseoleae) of the MP clade (Figure 1; Supplementary Figure S3), with the largest size being 22-kb (IV-C, Figure 3).…”

Section: Inversionsmentioning

confidence: 99%

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

et al. 2020

View full text Add to dashboard Cite

The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109-111 unique genes. We revealed four independent gene losses (ndhF, psbI, rps16, and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.

show abstract

Section: Inversionsmentioning

confidence: 99%

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

et al. 2020

View full text Add to dashboard Cite

show abstract

“…SSRs or microsatellites are tandemly repetitive DNA sequences that mostly measure <6 bp [ 33 , 34 ], are spread all over the genome [ 32 ], and are categorized as mono-, di-, tri-, tetra-, penta-, and hexanucleotide [ 35 ]. Chloroplast SSRs (cpSSRs) are very polymorphic, reproducible, and plentiful in the genome [ 36 ] and are mainly useful in plant genetic studies [ 37 ]. A total of 196 cpSSR markers were detected in the chloroplast genome of Streptocarpus teitensis , with mononucleotides (57.1%) being the majority, followed by the trinucleotides (33.2%), dinucleotides and tetranucleotides (both 4.1%), and finally the pentanucleotides (1.5%) ( Table 4 ).…”

Section: Resultsmentioning

confidence: 99%

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)

Kyalo

Gichira

et al. 2018

BioMed Research International

View full text Add to dashboard Cite

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

show abstract

“…As of now, there are 78,686 sequences (62,146 unigenes, 16,476 expressed sequence tags (EST)s and 61 nucleotides sequences) available in the National Center for Biotechnology Information (NCBI) database generated from early and late developing clusterbean seeds, and leaf transcriptomes generated from two clusterbean varieties using Illumina sequencing platform [ 15 , 16 ]. Recently, we have published the chloroplast genome of clusterbean [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)

Rawal

Kumar

S.V.

et al. 2017

Genes

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis

Cited by 48 publications

References 106 publications

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)

High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub)

Contact Info

Product

Resources

About