Genome surveying reveals the complete chloroplast genome and nuclear genomic features of the crocin-producing plant Gardenia jasminoides Ellis

Wang, Wencai; Shao, Fengqing; Deng, Xin; Liu, Yuanwei; Chen, Siyun; Li, Yongquan; Guo, Wei; Jiang, Qingbin; Hong, Lei; Zhang, Xianzhi

doi:10.1007/s10722-020-01056-6

Cited by 10 publications

(15 citation statements)

References 69 publications

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“…The GC content in the IR region was much higher than in the LSC and SSC region in C. spruceanum cp genome, probably due to the presence of eight ribosomal RNA (rRNA) genes in this region, which is consistent with previous analyses in other Ixoroideae [15,16], and in other angiosperms cp genomes [14,22,23]. The IR (A/B) region has always been considered consistent and stable in the cp genome, and it is also common in the evolution of plants with contraction or expansion events in the border region [16].…”

Section: Discussionsupporting

confidence: 89%

“…Our results are in agreement with other studies that report microsatellites markers for other Ixoroideae species such as C. arabica, C. canephora, and E. henryi [16]. However, we disagree with the results obtained by Wang et al [15] for G. jasminoides. With the identification of the SSR in the cp genome of C. spruceanum, we will be able to evaluate the polymorphism at the intraspecific level, as well as to evaluate the genetic diversity between and within the populations of C. spruceanum.…”

Section: Discussionsupporting

confidence: 86%

“…The C. spruceanum cp genome is in agreement with the characteristics of most angiosperm species in structure and gene content. In fact, the complete cp genome of C. spruceanum was 154,480pb, similar to other Ixoroideae genomes [15,17], with a quadripartite structure (LSC, SSC and two IR regions) which is a common characteristics in higher plants [11]. The annotation of C. spruceanum cp genome predicted 87 proteincoding genes (CDS), and similar patterns of protein-coding genes are also present in other Rubiaceae plants [16].…”

Section: Discussionmentioning

confidence: 54%

“…The IR (A/B) region has always been considered consistent and stable in the cp genome, and it is also common in the evolution of plants with contraction or expansion events in the border region [16]. Also, these results suggest that the cp genome in this subfamily had rather conserved genome organization [15,16]. We identified that in the seven sequences of the cp genome are some highly divergent regions including psbA-trnH-GUG, rps16-matK, atpI-atpH, ndhJ-rps4, rbcL-psaI, psaI-petA, ycf1-rps15, and rpl32-ndhF.…”

Section: Discussionmentioning

confidence: 64%

“…Until very recently, only a few complete chloroplast genome sequences for the Ixoroideae subfamily have been deposited to GenBank, with the very first being that of Coffea canephora in 2016. Nevertheless, with the development of Next Generation Sequencing (NGS), the chloroplast (cp) genome of most species of Ixoroideae subfamily has been obtained [2, [15][16][17], however, to date, cp genome of members of the genus Calycophyllum remained unknown. Thus, in the present study we sequenced for the first time the C. spruceanum chloroplast genome (accession number: OK326865.1) and compared with other members of the sub family Ixoroideae that are closely related.…”

Section: Discussionmentioning

confidence: 99%

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Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Saldaña¹,

Rodriguez-Grados²,

Chávez-Galarza³

et al. 2021

Preprint

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Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of de major lineages in the Rubiaceae family, and is an important timber tree, with origin in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct librar-ies. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes and 01 pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotide (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than invert regions. Finally, phylogenetic analysis resolved that C. spruceanum is a sister species to Emmenopterys henryi, and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 99%

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Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Saldaña¹,

Rodriguez-Grados²,

Chávez-Galarza³

et al. 2021

Preprint

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Unveiling molecular mechanisms of pigment synthesis in gardenia (Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis

Li,

Yu,

Gao

et al. 2024

Food Chemistry: Molecular Sciences

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Genome Survey Sequencing of the Medical Plant Dioscorea futschauensis: Genomic Characteristics Estimation and Genomic Resources Development

Luo,

Li,

et al. 2023

j biobased mat bioenergy

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Dioscorea futschauensis Uline ex R. Knuth, a perennial climbing herb belonging to the Stenophora section of the genus Dioscorea L. (Dioscoreaceae), originates from Southeast China and is highly regarded for its medicinal properties. Despite its medicinal significance, the absence of genomic information has impeded the effective utilization and conservation of this species. Here, we conducted genome survey sequencing of D. futschauensis to unveil its genomic characteristics and identify species-specific genomic markers, including whole plastome sequence, plastome-divergent hotspots, single-copy nuclear genes and polymorphic nuclear SSRs. The genome of D. futschauensis was approximated to be 1392.76 Mb in length, accompanied by a substantial heterozygosity rate of 1.75% and a repeat content of 67.43%. Comparative plastome analysis illuminated the conserved genome structure and gene content within D. futschauensis, and revealed four highly divergent hotspots (atpF intron, psbA-matK, matK -rps16, and rrn16-trnI) that could serve as molecular markers for D. futschauensis and its closely related species. Furthermore, more than 200 single-copy nuclear genes and 78 polymorphic nuclear SSRs were identified within D. futschauensis. Overall, the comprehensive genomic information and abundant genetic resources provided herein will not only facilitate extended research in the realms of population genetics, phylogenetics and conservation biology of D. futschauensis, but also hold considerable value for its cultivation and molecular breeding applications.

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Genome surveying reveals the complete chloroplast genome and nuclear genomic features of the crocin-producing plant Gardenia jasminoides Ellis

Cited by 10 publications

References 69 publications

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Unveiling molecular mechanisms of pigment synthesis in gardenia (Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis

Genome Survey Sequencing of the Medical Plant Dioscorea futschauensis: Genomic Characteristics Estimation and Genomic Resources Development

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