Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

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The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9121692 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1692

Author(s):

Li Gu ◽

Ting Su ◽

Ming-Tai An ◽

Guo-Xiong Hu

Keyword(s):

Phylogenetic Analysis ◽

Sequence Similarity ◽

Single Copy ◽

Structural Features ◽

Rrna Genes ◽

Trna Genes ◽

Sequencing Data ◽

High Sequence Similarity ◽

Plastid Genomes ◽

Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

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Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽

10.3390/molecules23092137 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2137 ◽

Cited By ~ 6

Author(s):

Xiang-Xiao Meng ◽

Yan-Fang Xian ◽

Li Xiang ◽

Dong Zhang ◽

Yu-Hua Shi ◽

...

Keyword(s):

Gc Content ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Chloroplast Genomes ◽

Close Relationship ◽

Cp Genome ◽

Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

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De Novo Genome Assembly of Next-Generation Sequencing Data

Compendium of Plant Genomes - The Brassica rapa Genome ◽

10.1007/978-3-662-47901-8_4 ◽

2015 ◽

pp. 41-51

Author(s):

Min Liu ◽

Dongyuan Liu ◽

Hongkun Zheng

Keyword(s):

Next Generation Sequencing ◽

Genome Assembly ◽

De Novo ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

De Novo Genome Assembly ◽

Generation Sequencing

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Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae

Plants ◽

10.3390/plants9101354 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1354

Author(s):

Slimane Khayi ◽

Fatima Gaboun ◽

Stacy Pirro ◽

Tatiana Tatusova ◽

Abdelhamid El Mousadik ◽

...

Keyword(s):

Chloroplast Genome ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Important Species ◽

Complete Chloroplast Genome ◽

Argania Spinosa ◽

Protein Coding Genes ◽

Cp Genome

Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.

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Analyzing population structure for forensic STR markers in next generation sequencing data

Forensic Science International Genetics ◽

10.1016/j.fsigen.2020.102364 ◽

2020 ◽

Vol 49 ◽

pp. 102364

Author(s):

Sanne E. Aalbers ◽

Michael J. Hipp ◽

Scott R. Kennedy ◽

Bruce S. Weir

Keyword(s):

Population Structure ◽

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Str Markers ◽

Generation Sequencing

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Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

10.21203/rs.3.rs-60093/v4 ◽

2020 ◽

Author(s):

Gurusamy Raman ◽

KyuTae Park ◽

Joo Hwan Kim ◽

SeonJoo Park

Keyword(s):

Genome Sequence ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Rrna Genes ◽

Trna Genes ◽

Comparative Analyses ◽

Sister Clade ◽

Mutational Hotspots ◽

Phylogenetic Implications ◽

Cp Genome

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

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Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9030296 ◽

2020 ◽

Vol 9 (3) ◽

pp. 296 ◽

Cited By ~ 3

Author(s):

Jacinta N. Munyao ◽

Xiang Dong ◽

Jia-Xin Yang ◽

Elijah M. Mbandi ◽

Vincent O. Wanga ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Important Species ◽

Genomic Resources ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Cp Genome ◽

High Level

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

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Scalable Framework for the Analysis of Population Structure Using the Next Generation Sequencing Data

Lecture Notes in Computer Science - Foundations of Intelligent Systems ◽

10.1007/978-3-319-60438-1_46 ◽

2017 ◽

pp. 471-480 ◽

Cited By ~ 1

Author(s):

Anastasiia Hryhorzhevska ◽

Marek Wiewiórka ◽

Michał Okoniewski ◽

Tomasz Gambin

Keyword(s):

Population Structure ◽

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing

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The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Forests ◽

10.3390/f11020158 ◽

2020 ◽

Vol 11 (2) ◽

pp. 158

Author(s):

Jianshuang Shen ◽

Xueqin Li ◽

Xiangtao Zhu ◽

Xiaoling Huang ◽

Songheng Jin

Keyword(s):

Western Europe ◽

Size Structure ◽

Gc Content ◽

Purifying Selection ◽

Rrna Genes ◽

Biological Research ◽

Genome Comparison ◽

Trna Genes ◽

Protein Coding ◽

Cp Genome

Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.

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