Complete plastid genome sequence of goosegrass (Eleusine indica) and comparison with other Poaceae

Zhang, Hui; Hall, Nathan; McElroy, J. Scott; Lowe, Elijah K.; Goertzen, Leslie R.

doi:10.1016/j.gene.2016.11.038

Cited by 19 publications

(17 citation statements)

References 39 publications

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“…Our ndings for the A and B genome donors concur with past research [10,13,[48][49][50]. The kS values show evidence of ancient Poaceae genome duplications [51][52][53], and suggested that when Eleusine coracana arose 1.1 mya at the divergence of Eleusine indica and the A subgenome around the same time as Eragrostis tef [25].…”

Section: Discussionsupporting

confidence: 90%

“…Past work designating the genome donors of E. coracana has been limited to a few loci [8,11,12], or organellar genomes [50]. Our implementation of a genome guided orthology approach [54] is the most comprehensive treatment of this genus to date and the rst to include a sample for each likely B genome donor since Eleusine multi ora and Eleusine jaegeri can be ruled out as genome donors based on number of chromosomes alone and Eleusine semisterilis has never been considered a strong contender owing to its morphological divergence [55].…”

Section: Discussionmentioning

confidence: 99%

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Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Hall

Patel

McElroy

et al. 2020

Preprint

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Background: Finger millet (Eleusine coracana 2n=4x=36 ) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs. Results: We produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A , 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes. Examination of expression within the circadian rhythm pathway suggests A subgenomic preference. Conclusion: The evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Hall

Patel

McElroy

et al. 2020

Preprint

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“…The IR regions have been observed to be potential distinguishing features among most angiosperms, as their expansions or contractions in or out of the single-copy regions are attributed to the different chloroplast genome sizes [ 43 , 44 ]. The order in which genes are arranged in the junctions between the genome regions has also differentiated between species [ 45 ].…”

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

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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.

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“…Several studies have indicated that chloroplast genomes and cpSSRs have enormous potential (Zhang et al 2017) and they are an important tool for plant biologists and breeders in assessing genetic diversity (Doorduin et al 2011), spatial genetic structure (Islam et al 2015), evolutionary history, and hybridization in native and improved species (Ebert andPeakall 2009, Doorduin et al 2011). Thus, our analysis provides a rich database for researchers that can be used to study these Eucalyptus species across a wide range of scientific disciplines.…”

Section: Resultsmentioning

confidence: 99%

Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

Andrade

Perek

Pereira

et al. 2018

Crop Breed. Appl. Biotechnol.

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In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta-and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.

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Complete plastid genome sequence of goosegrass (Eleusine indica) and comparison with other Poaceae

Cited by 19 publications

References 39 publications

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

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

Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

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