Phylogenomic analysis of the chloroplast genome of the green-tide forming macroalga Ulva intestinalis Linnaeus (Ulvophyceae, Chlorophyta)

Kapur (Dryobalanops aromatica) is an important dipterocarp species currently classified as vulnerable by the IUCN Red List Threatened Species. Science-based conservation and restoration efforts are needed, which can be supported by new genomic data generated from new technologies, including MinION Oxford Nanopore Technology (ONT). ONT allows affordable long-read DNA sequencing, but this technology is still rarely applied to native Indonesian forest trees. Therefore, this study aimed to generate whole genome datasets through ONT and use part of these data to construct the draft of the chloroplast genome and analyze the universal DNA barcode-based genetic relationships for D. aromatica. The method included DNA isolation, library preparation, sequencing, bioinformatics analysis, and phylogenetic tree construction. Results showed that the DNA sequencing of D. aromatica resulted in 1.55 Gb of long-read DNA sequences from which a partial chloroplast genome (148,856 bp) was successfully constructed. The genetic relationship was analyzed using two selected DNA barcodes (rbcL and matK), and its combination showed that species of the genus Dryobalanops had a close relationship as indicated by adjacent branches between species. The phylogenetic tree of matK and the combination of the matK and rbcL genes showed that D. aromatica was closely related to Dryobalanops rappa, whereas the rbcL gene showed group separation between D. aromatica and D. rappa. Therefore, a combination of the matK and rbcL genes is recommended for future use in the phylogenetic or phylogenomic analysis of D. aromatica.

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Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae

Scientific Reports ◽

10.1038/s41598-018-27453-7 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 15

Author(s):

Bin Li ◽

Yongqi Zheng

Keyword(s):

Chloroplast Genome ◽

Dynamic Evolution ◽

Phylogenomic Analysis

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Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

BMC Genomics ◽

10.1186/s12864-021-07590-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wenpan Dong ◽

Yanlei Liu ◽

Chao Xu ◽

Yongwei Gao ◽

Qingjun Yuan ◽

...

Keyword(s):

Chloroplast Genome ◽

Ribosomal Rna ◽

Leaf Size ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Transfer Rnas ◽

Chloroplast Genomes ◽

Conserved Gene ◽

Rna Genes ◽

Simple Sequence

Abstract Background Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. Results The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. Conclusions The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.

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Peach chloroplast genome variation architecture and phylogenomic signatures of cpDNA introgression in Prunus

Canadian Journal of Plant Science ◽

10.1139/cjps-2019-0129 ◽

2019 ◽

Vol 99 (6) ◽

pp. 885-896

Author(s):

Mohamed Hamdy Amar ◽

Mahmoud Magdy ◽

Lu Wang ◽

Hui Zhou ◽

Beibei Zheng ◽

...

Keyword(s):

Chloroplast Genome ◽

Prunus Persica ◽

Gc Content ◽

Size Variation ◽

Intergenic Spacer ◽

Phylogenomic Analysis ◽

Single Nucleotide Variants ◽

Prunus Species ◽

Genome Size Variation ◽

Essential Information

The complete chloroplast genome of peach provides essential information required for the assessment of phylogenetic relationships among Prunus species. Here, we compared the complete chloroplast DNA (cpDNA) genome between two peach cultivars and a wild relative, Prunus mira. The cpDNA genomes of the three peach specimens ranged from 157 330 to 157 744 bp in length and all contained 133 genes and 128 intergenic spacer (IGS) regions with an average GC content of 36.8%. The cpDNA genome of peach contained approximately 600 simple sequence repeats (SSRs), with hexa-nucleotide repeats being the most frequent microsatellites. Most SSRs have undergone divergence between cultivated and wild peaches. A total of 331 single nucleotide variants were identified in the cpDNA genomes. Fifty-one multiple-base pair indels were detected, which are mainly responsible for the cpDNA genome size variation. The cpDNA genomes contained 45 hypervariable regions, with 78% in the large single copy region (LSC). Phylogenomic analysis revealed that Prunus persica is more closely related to Prunus kansuensis than to other wild relatives, and a frequency of introgression of the chloroplast genome between Prunus species was deduced. Collectively, various genetic variations in the cpDNA genomes can serve as molecular markers for genomic studies of Prunus species, such as DNA barcoding, phylogeny, and systematics.

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Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis

PLoS ONE ◽

10.1371/journal.pone.0184196 ◽

2017 ◽

Vol 12 (9) ◽

pp. e0184196 ◽

Cited By ~ 8

Author(s):

Chuner Cai ◽

Lingke Wang ◽

Lingjie Zhou ◽

Peimin He ◽

Binghua Jiao

Keyword(s):

Comparative Analysis ◽

Chloroplast Genome ◽

Green Tide ◽

Complete Chloroplast Genome

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A relative contribution of carbon from green tide algae Cladophora glomerata and Ulva intestinalis in the coastal food webs in the Neva Estuary (Baltic Sea)

Marine Pollution Bulletin ◽

10.1016/j.marpolbul.2017.10.032 ◽

2018 ◽

Vol 126 ◽

pp. 43-50 ◽

Cited By ~ 8

Author(s):

Sergey M. Golubkov ◽

Nadezhda A. Berezina ◽

Yulia I. Gubelit ◽

Anna S. Demchuk ◽

Mikhail S. Golubkov ◽

...

Keyword(s):

Baltic Sea ◽

Food Webs ◽

Green Tide ◽

Cladophora Glomerata ◽

Neva Estuary ◽

Relative Contribution ◽

Ulva Intestinalis

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Variation in germling growth in the green tide–forming alga Ulva intestinalis (Chlorophyta) in response to gradients in salinity, temperature, light, and nutrients

Journal of Applied Phycology ◽

10.1007/s10811-021-02563-4 ◽

2021 ◽

Author(s):

Ju-Hyoung Kim ◽

Zi Xu Zhao ◽

Young Sik Kim

Keyword(s):

Green Tide ◽

Ulva Intestinalis

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The complete chloroplast genome of Chinese medicine (Psoralea corylifolia Linn): Molecular Structures, barcoding analysis, and phylogenetic Analysis

10.1101/587758 ◽

2019 ◽

Author(s):

Wei Tan ◽

Han Gao ◽

Huanyu Zhang ◽

Xiaolei Yu ◽

Xiaoxuan Tian ◽

...

Keyword(s):

Chinese Medicine ◽

Chloroplast Genome ◽

Tandem Repeats ◽

Single Copy ◽

Molecular Structures ◽

Phylogenomic Analysis ◽

Evolutionary Status ◽

Psoralea Corylifolia ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes

AbstractPsoralea corylifoliais one kind of traditional Chinese medicine used in China widely. In this study, we sequence the complete chloroplast genome ofP. corylifolia, which is 153,114 bp in size and includes a pair of inverted repeats regions of 25,557 bp interspersed by a small single copy of 17,885 bp and a large single copy of 84,115 bp region. Approximately 98 simple sequence repeats, 14 forward, 2 reverse, 2 complement, 32 palindromic and 49 tandem repeats are identified in theP. corylifoliachloroplast genome. The chloroplast genomes ofP. corylifoliaand threeGlycinespecies are conserved in gene order and content, but show high diversity within intergenic spacers.P. corylifoliawith threeGlycinespecies in Papilionoideae fall into the same clade based on 75 conserved coding-protein genes phylogenomic analysis. Moreover, four chloroplast DNA regions (ycf1, matK, accD, ndhF) can serve as the barcodes. In general, our findings will dedicate to better comprehension of the genome aspect as well as evolutionary status ofP. corylifolia.

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Plastid phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

10.21203/rs.3.rs-119007/v1 ◽

2020 ◽

Author(s):

Wenpan Dong ◽

Yanlei Liu ◽

Chao Xu ◽

Yongwei Gao ◽

Zhixiang Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Ribosomal Rna ◽

Leaf Size ◽

Phylogenomic Analysis ◽

Genome Sequences ◽

Protein Coding ◽

Transfer Rnas ◽

Conserved Gene ◽

Rna Genes ◽

Simple Sequence

Abstract Background: Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and identify variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genome. Results: The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order displayed and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, such as matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. Conclusions: The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify species accurately.

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