FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2977185725> ?p ?o ?g. }

• W2977185725 endingPage "e7558" @default.
• W2977185725 startingPage "e7558" @default.
• W2977185725 abstract "Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars." @default.
• W2977185725 created "2019-10-03" @default.
• W2977185725 creator A5002300371 @default.
• W2977185725 creator A5010482357 @default.
• W2977185725 creator A5021050305 @default.
• W2977185725 creator A5042605799 @default.
• W2977185725 date "2019-09-24" @default.
• W2977185725 modified "2023-10-15" @default.
• W2977185725 title "The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics" @default.
• W2977185725 cites W1031578623 @default.
• W2977185725 cites W1767772592 @default.
• W2977185725 cites W1803102843 @default.
• W2977185725 cites W1904671705 @default.
• W2977185725 cites W1969042907 @default.
• W2977185725 cites W1970571754 @default.
• W2977185725 cites W1970936047 @default.
• W2977185725 cites W1973000575 @default.
• W2977185725 cites W1981364246 @default.
• W2977185725 cites W1982855075 @default.
• W2977185725 cites W1991330646 @default.
• W2977185725 cites W1994390368 @default.
• W2977185725 cites W1996423252 @default.
• W2977185725 cites W1998994980 @default.
• W2977185725 cites W2007668764 @default.
• W2977185725 cites W2012873070 @default.
• W2977185725 cites W2022472106 @default.
• W2977185725 cites W2030383295 @default.
• W2977185725 cites W2033713984 @default.
• W2977185725 cites W2037586962 @default.
• W2977185725 cites W2037689767 @default.
• W2977185725 cites W2055043387 @default.
• W2977185725 cites W2055350245 @default.
• W2977185725 cites W2060512149 @default.
• W2977185725 cites W2063732750 @default.
• W2977185725 cites W2069131373 @default.
• W2977185725 cites W2073555865 @default.
• W2977185725 cites W2074278283 @default.
• W2977185725 cites W2079620138 @default.
• W2977185725 cites W2081670102 @default.
• W2977185725 cites W2083248306 @default.
• W2977185725 cites W2084074554 @default.
• W2977185725 cites W2089047063 @default.
• W2977185725 cites W2090392412 @default.
• W2977185725 cites W2090547827 @default.
• W2977185725 cites W2091110471 @default.
• W2977185725 cites W2091448229 @default.
• W2977185725 cites W2092124576 @default.
• W2977185725 cites W2092135605 @default.
• W2977185725 cites W2094939159 @default.
• W2977185725 cites W2097019746 @default.
• W2977185725 cites W2097659302 @default.
• W2977185725 cites W2097958700 @default.
• W2977185725 cites W2101291993 @default.
• W2977185725 cites W2101510328 @default.
• W2977185725 cites W2102278945 @default.
• W2977185725 cites W2103441770 @default.
• W2977185725 cites W2104789942 @default.
• W2977185725 cites W2106850544 @default.
• W2977185725 cites W2107158607 @default.
• W2977185725 cites W2108234281 @default.
• W2977185725 cites W2113032422 @default.
• W2977185725 cites W2113180960 @default.
• W2977185725 cites W2114289095 @default.
• W2977185725 cites W2114900941 @default.
• W2977185725 cites W2116924284 @default.
• W2977185725 cites W2117131162 @default.
• W2977185725 cites W2119180969 @default.
• W2977185725 cites W2120902911 @default.
• W2977185725 cites W2121851042 @default.
• W2977185725 cites W2124281279 @default.
• W2977185725 cites W2126149189 @default.
• W2977185725 cites W2128285406 @default.
• W2977185725 cites W2128841626 @default.
• W2977185725 cites W2129312896 @default.
• W2977185725 cites W2130362098 @default.
• W2977185725 cites W2130834689 @default.
• W2977185725 cites W2130869024 @default.
• W2977185725 cites W2132023322 @default.
• W2977185725 cites W2132541664 @default.
• W2977185725 cites W2132629607 @default.
• W2977185725 cites W2136246388 @default.
• W2977185725 cites W2136750557 @default.
• W2977185725 cites W2137482052 @default.
• W2977185725 cites W2139229065 @default.
• W2977185725 cites W2139736670 @default.
• W2977185725 cites W2141292707 @default.
• W2977185725 cites W2142678478 @default.
• W2977185725 cites W2146058063 @default.
• W2977185725 cites W2146119511 @default.
• W2977185725 cites W2150934173 @default.
• W2977185725 cites W2151831732 @default.
• W2977185725 cites W2153325555 @default.
• W2977185725 cites W2155015138 @default.
• W2977185725 cites W2158492424 @default.
• W2977185725 cites W2158714788 @default.
• W2977185725 cites W2166243950 @default.
• W2977185725 cites W2166265186 @default.
• W2977185725 cites W2168696662 @default.

• next