Comparative plastome analyses and genomic resource development in wild rice (Zizania spp., Poaceae) using genome skimming data

Lu, Ruisen; Chen, Min; Feng, Yu; Ni, Yuan; Zhang, Yanmei; Cao, Minxu; Liu, Jia; Wang, Yue; Hang, Yue‐Yu; Sun, Xiaoqin

doi:10.1016/j.indcrop.2022.115244

Cited by 14 publications

(17 citation statements)

References 68 publications

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“…Previous studies have reported that plastomes within a species are highly conserved in terms of genomic structure, GC content, gene content, and the synteny of gene order [ 26 , 28 ], with D. alata being no exception in this regard. The pan-plastome of D. alata constructed here indicated that all 52 accessions (153,114–153,161 bp) from different geographical areas possessed the typical quadripartite structure of land plant plastomes, with a pair of IR regions (25,464 bp) separating the LSC (83,351–83,415 bp) and SSC (18,815–18,836 bp) regions, and encoded the same 113 unique genes, including 79 PCGs, 30 tRNAs, and 4 rRNAs ( Figure 1 , Table S1 ).…”

Section: Discussionmentioning

confidence: 99%

“…Given that the difference in the IRA/SSC boundary between D. polystachya and the other plastomes is very trivial ( Figure 3 ), these results provided a further proof of the conserved nature of the Enantiophyllum plastomes. In addition, in contrast to most monocots, with their IRs expanding and encompassing the rps19 - trn H gene cluster (e.g., Arecales, Dasypogonaceae, Poales, Zingiberales, Asparagales, and Commelinales) [ 28 , 32 ], all the LSC/IRA boundaries of the Enantiophyllum plastomes were located within the rps19 gene ( Figure 3 ).…”

Section: Discussionmentioning

confidence: 99%

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Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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“…This could be attributed to copy correction between IR sequences by gene conversion, and the abundance of conserved rRNA genes in the IRs ( Khakhlova and Bock, 2006 ). In addition, the protein-coding regions were found to be more conserved than non-coding regions (including intergenic spacers and introns), which were likely to be subject to natural selection ( Shaw et al., 2007 ; Lu et al., 2022 ).…”

Section: Resultsmentioning

confidence: 99%

“…With the rapid development of next generation sequencing (NGS) technologies, it is cheap and fast to obtain low-coverage (~0.1–10×) of the whole genome sequencing data (or called genome skimming data), which could provide sufficient data for complete plastome assemblies ( Straub et al., 2012 ; Twyford and Ness, 2017 ; Jin et al., 2020 ). Besides, the assembled nuclear scaffolds from low-coverage whole genome sequencing data could be used for mining polymorphic nuclear SSRs (nSSRs) (e.g., Liu et al., 2018 ; Xia et al., 2018 ; Lu et al., 2022 ). Here, we performed low-coverage whole genome shotgun sequencing for 11 Stenophora species/subspecies (i.e., D. banzhuana Pei & Ting, D. biformifolia Pei & Ting, D. collettii Hook.f., D. deltoidea Wall., D. futschauensis Uline ex R.Knuth, D. gracillima Miq., D. nipponica Makino, D. nipponica subsp.…”

Section: Introductionmentioning

confidence: 99%

Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference

Sun

Chen

et al. 2023

Front. Plant Sci.

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Dioscorea sect. Stenophora (Dioscoreaceae) comprises about 30 species that are distributed in the temperate and subtropical regions of the Northern Hemisphere. Despite being evolutionarily “primitive” and medically valuable, genomic resources and molecular studies of this section are still scarce. Here, we conducted low-coverage whole genome sequencing of 11 Stenophora species/subspecies to retrieve their plastome information (whole plastome characteristics, plastome-divergent hotspots, plastome-derived SSRs, etc.) and polymorphic nuclear SSRs, as well as performed comparative plastome and phylogenetic analyses within this section. The plastomes of Stenophora species/subspecies ranged from 153,691 bp (D. zingiberensis) to 154,149 bp (D. biformifolia) in length, and they all contained the same 114 unique genes. All these plastomes were highly conserved in gene structure, gene order and GC content, although variations at the IR/SC borders contributed to the whole length differences among them. The number of plastome-derived SSRs among Stenophora species/subspecies varied from 74 (D. futschauensis) to 93 (D. zingiberensis), with A/T found to be the most frequent one. Seven highly variable regions and 12 polymorphic nuclear SSRs were identified in this section, thereby providing important information for further taxonomical, phylogenetic and population genetic studies. Phylogenomic analyses based on whole plastome sequences and 80 common protein coding genes strongly supported D. biformifolia and D. banzhuana constituted the successive sister species to the remaining sampled species, which could be furtherly divided into three clades. Overall, this study provided a new perspective for plastome evolution of Stenophora, and proved the role of plastome phylogenomic in improving the phylogenetic resolution in this section. These results also provided an important reference for the protection and utilization of this economically important section.

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“…Chloroplast genomes within a species are highly conserved in terms of genomic structure, gene content, gene order, and GC content [ 50 , 51 ], with P. fortuneana being no exception in this regard. All three individuals of P. fortuneana (two flower phenotypes) possessed the typical quadripartite structure of land plant chloroplast genomes, with a pair of IR regions (26,350–26,355 bp) separating LSC (88,316–88,393 bp) and SSC (19,344–19,348 bp) regions, and encoded 113 identical unique genes, including 79 PCGs, 30 tRNAs, and four rRNAs ( Figure 2 , Table 1 and Table 2 ).…”

Section: Discussionmentioning

confidence: 99%

Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny

Ding

et al. 2022

Genes

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Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

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Comparative plastome analyses and genomic resource development in wild rice (Zizania spp., Poaceae) using genome skimming data

Cited by 14 publications

References 68 publications

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference

Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny

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