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Phylogeny of P. troglodytes troglodytes and closely related
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The complete chloroplast sequence of the Chikusichloa aquatica was determined in this study. The genome consists of 136 563 bp containing a pair of inverted repeats (IRs) of 20 837 bp, which was separated by a large single-copy region and a small single-copy region of 82 315 bp and 33 411 bp, respectively. The C. aquatica cp genome encodes 111 func...
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... (ML) with the Hasegawa–Kishino–Yano (HKY) model (lowest BIC score 1⁄4 3846) and a gamma distribution (5 discrete gamma categories), which was reconstructed using the MEGA6 (Tamura et al., 2013). One thousand bootstrap replicates were set for each analysis to get the confident supports. Our obtained phylogeny showed that the P. t. troglodytes mitochondrial genome formed a cluster with the other three Pan troglodytes genomes (Figure 1). Our result is consistent to previous report (Inoue et al., 2007), providing evidence that the genus Pan is closely related to the genus Homo ...
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Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica , the first in the distinctive family Helwingiaceae and only the second genus to be sequenced...
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... Chloroplasts are typically AT-rich, and the GC content of the P. miliaceum chloroplast was similar to values previously reported for most other Gramineae species (e.g. 39.0% in Chikusichloa aquatica; Zhang et al. 2015). The LSC and SSC contained 81,918 bp and 12,565 bp, respectively, while the IR was 22,723 bp in length. ...
Common millet (Panicum miliaceum) is the most valuable and ancient domesticated important crops in the world. We compared five common millet complete chloroplast genomes. A complete map of the variability across the genomes of the five common millet was produced that included single nucleotide variants, InDels, and structural variants, as well as differences in simple sequence repeats and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into single monophyly with a 100% bootstrap value. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in common millet.
... or in the context of detailed phylogenomic analyses of different grass lineages, including the PACMAD clade (Cotton et al., 2015;Teisher et al., 2017), Bambusoideae (Wu et al., 2015;Wysocki et al., 2015;Attigala et al., 2016;Vieira et al., 2016;Zhang & Chen, 2016), Aristidoideae (Besnard et al., 2014), Brachypodieae (Sancho et al., 2017), early diverging grasses (Burke et al., 2016a), Panicoideae (Burke et al., 2016b), Chloridoideae , Zea (Orton et al., 2017), Micrairoideae , Pooideae (Saarela et al., 2015) and Oryzeae (Kim et al., 2015;Liu et al., 2016;Wu & Ge, 2016;Zhang et al., 2016aZhang et al., , 2016b. Phylogenomic analyses of plastomes have contributed increased resolution and support for many relationships within and among grass subfamilies compared with earlier singleand multi-gene plastid studies. ...
... Taxon sampling includes 15 new (Table 1) and 235 plastomes obtained from GenBank (Asano et al., 2004;Saski et al., 2007;Bortiri et al., 2008;Diekmann et al., 2009;Leseberg & Duvall, 2009;Wu et al., 2009;Wu & Ge, 2012;Nock et al., 2011;Young et al., 2011;Zhang, Ma & Li, 2011;Zhang et al., 2016b;Burke, Grennan & Duvall, 2012;Burke et al., 2014Burke et al., , 2016aBurke et al., , 2016bWaters et al., 2012;Besnard et al., 2013Besnard et al., , 2014Hand et al., 2013;Gornicki et al., 2014;Jones, Burke & Duvall, 2014;Lee et al., 2014;Ma et al., 2014Ma et al., , 2015Mariac et al., 2014;Middleton et al., 2014;Ye et al., 2014;Cotton et al., 2015;Gogniashvili et al., 2015;Kim et al., 2015;Lundgren et al., 2015;Rousseau-Gueutin et al., 2015;Saarela et al., 2015;Wambugu et al., 2015;Wang & Gao, 2015;Wysocki et al., 2015;Attigala et al., 2016;Duvall et al., 2016Duvall et al., , 2017Gao, Li & Gao, 2016;Nah et al., 2016) (Table S1). Plastomes not available on GenBank as of 19 November 2015 were not included in our analyses, unless generated by us. ...
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
... In addition to these species, many wild relatives in the Oryzeae tribe possess enormously useful genetic resources for improving rice breeding through increasing yields [9] and providing tolerance from environmental stress [10]. While the species in the Oryzinae tribe have been studied in depth with regard to their genetic importance [2,11,12,13], the species in Zizaniinae have not been as thoroughly examined, except for the organelle genomes [14,15,16]. Chikusichloa is one such example of a genus from Zizaniinae for which we have only limited knowledge regarding the chloroplast genome. ...
... In this study, by employing traditional Sanger sequencing and sets of conserved universal primers from grass species, we assembled a high quality complete chloroplast genome of Chikusichloa mutica and deposited the annotated sequence into the NCBI database. We also conducted a comprehensive comparison with the other published chloroplast genome of C. aquatica (KR078265) [16] to detect all polymorphisms between the two whole chloroplast genomes. Utilizing the whole chloroplast, we reconstructed the phylogenetic relationships of all rice tribe species and compared their genomic features and structural variation. ...
... To compare the polymorphisms in detail between the whole chloroplast genomes within Chikusichloa, the published genome data from C. aquatica (KR078265) [16] was employed for comparison with our newly completed chloroplast genome of C. mutica. Based on the conserved structure of chloroplast genomes within the grass family [14,37], the two genome sequences could be aligned by synteny. ...
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.
... Chloroplasts are typically AT rich, and the GC content of the P. miliaceum chloroplast was similar to values previously reported for most other Gramineae species (e.g. 39.0% in Chikusichloa aquatica; Zhang et al. 2015). The LSC and SSC contained 81,918 bp and 12,565 bp, respectively, while the IR was 22,723 bp in length. ...
Panicum miliaceum is the most important and ancient domesticated crops in the world. The complete chloroplast genome of P. miliaceum was sequenced using the Illumina Hiseq platform (Illumina Inc., San Diego, CA). The chloroplast genome of P. miliaceum was 139,929 bp in length, with 38.60% GC content. It contains a pair of inverted repeats (IRs) (22,723 bp) which were separated by a large single copy (LSC) (81,918 bp) and a small single copy region (SSC) (12,565 bp). A total of 132 genes were annotated, which included 84 protein coding genes, 40 tRNA genes and eight rRNA genes. The neighbour-joining (NJ) phylogenetic analysis with the reported chloroplast genomes showed that P. miliaceum chloroplasts are most closely related to those of the Gramineae family.
Ophiocordycipitaceae is a diverse fungal family comprising multiple ecologically, economically, medicinally, and culturally important fungal species; however, only four species of the family have available mitochondrial genomes (mitogenomes). In this study, the complete mitogenome of the nematode endoparasitic fungus Hirsutella vermicola in Ophiocordycipitaceae was sequenced, and a comparative mitogenomic analysis of Ophiocordycipitaceae was performed. We found that the 53,793-bp circular mitogenome of H. vermicola, except for standard fungal mitochondrial genes, harbors seven introns acquired possibly through lateral transfer from other fungi and three free-standing open reading frames (ORFs) coding for hypothetical proteins. Phylogenetic analysis based on concatenated mitochondrial protein sequences confirmed its placement in Ophiocordycipitaceae. Comparison on five mitogenomes of Ophiocordycipitaceae revealed great variation on their sizes, from 35.2 kb in Tolypocladium ophioglossoides to 157.5 kb in Ophiocordyceps sinensis, mainly due to variable numbers of introns (from 7 to 54) as well as variable lengths of intergenic regions. The five mitogenomes, however, are highly syntenic to each other in terms of gene order, the presence of an intronic ORF encoding ribosomal protein S3 within rnl, and the nad2/nad3 joining pattern. Our study is the first report of the mitogenome of H. vermicola and has facilitated the understanding of mitogenome evolution of Ophiocordycipitaceae.
As part of a genome sequencing project for Tolypocladium ophioglossoides (T. ophioglossoides), a complete mitochondrial (mt) genome was assembled as a single circular dsDNA of 35,159 bp. Conserved genes including the large and small rRNA subunits, 25 tRNA and 15 protein-coding genes, were identified. In addition, 4 non-conserved open reading frames (ncORFs) in the intergenic and intronic regions were also identified. Transcription analyses using RNA-seq validated the expression of most conserved genes and ncORFs. Seven introns (groups I and II) were found within conserved genes, accounting for 21% of the mitogenome. All structural genes are located on one strand and are apparently transcribed in one direction. The complete mt genomes of T. ophioglossoides would be useful for future investigation of genetics, evolution and clinical identification of Tolypocladium species.
In this study, the complete mitochondrial genome of the White-Nose Syndrome pathogen, Pseudogymnoascus destructans (=Geomyces destructans), is sequenced. The circular mitochondrial genome is 32,181 bp long and encodes 13 standard proteins, 2 ribosomal RNA subunits, and 27 tRNAs. The genome contains two introns located within the cytochrome c oxidase subunit 1 gene (cox1) and the large ribosomal RNA subunit (rrnl), with each intron encoding one gene, orf110 and rps3, respectively. Phylogenetic analysis of the concatenated mitochondrial protein-coding genes of P. destructans and close representatives in Leotiomycetes showed that P. destructans was closely related to Pseudogymnoascus pannorum, consistent with nuclear genes.
