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Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome

2019-03-01T00:00:00Z

Title: Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome Authors: Shin, Seung Chul; Kim, Hyun; Lee, Jun Hyuck; Kim, Han-Woo; Park, Joonho; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Ji Hee; Lee, Hyoungseok; Kim, Sanghee Abstract: Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information.

The mitochondrial genome of the ciliate Pseudourostyla cristata (Ciliophora, Urostylida)

2019-01-01T00:00:00Z

Title: The mitochondrial genome of the ciliate Pseudourostyla cristata (Ciliophora, Urostylida) Authors: Park, Kyung-Min; Min, Gi-Sik; Kim, Sanghee Abstract: The mitochondrial genomes (mitogenomes) of ciliates are linear and relatively large (<80 kb). Until now, only 11 ciliate mitogenomes, either partial or complete, have been reported. The aim of the present study was to characterize the mitogenome of Pseudourostyla cristata (Ciliophora, Urostylida). The resulting mitogenome represents the first complete mitogenome for order Urostylida and is the largest sequenced ciliate mitogenome (~76 kb), containing 31 protein-coding genes, nine transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and 21 unclassified open reading frames. Among the 11 ciliates whose mitogenomes have been identified, the mitogenome of P. cristata is most similar to that of Oxytricha trifallax, which is in the same subclass. However, the mitogenome of P. cristata is missing two genes (nad3 and nad6) and three split genes (nad4, nad5, and rpl6) that are found in the mitogenome of O. trifallax. Furthermore, the locations of the protein-coding and tRNA genes in P. cristata are different than those of the same genes in either Euplotes minuta or E. crassus, even though the species belong to the same class. This suggests that mitogenome structure is unlikely conserved in class level phylogenetic comparison.

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments

2018-11-29T00:00:00Z

Title: Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments Authors: Chun, Jongsik; Lee, Hong Kum; Shin, Seung Chul; Hong, Soon Gyu; Choi, Hakkyum; Noh, Hyun-Ju; Kim, Mincheol; Hwang, Chung Yeon; Lee, Jae Il; Hwang, Kyuin; Lee, Yung Mi Abstract: Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8？40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediment. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.

Morphology and phylogeny of a new species, Uroleptus (Caudiholosticha)antarctica n. sp. (Ciliophora, Hypotricha) from Greenwich Island in Antarctica

2018-09-01T00:00:00Z

Title: Morphology and phylogeny of a new species, Uroleptus (Caudiholosticha)antarctica n. sp. (Ciliophora, Hypotricha) from Greenwich Island in Antarctica Authors: Park, Kyung-Min; Min, Gi-Sik; Kim, Sanghee Abstract: This paper describes the morphological features based on standard methods and estimates their phylogenetic position using small subunit ribosomal RNA (SSU rRNA) sequences of a Uroleptus (Caudiholosticha) antarctica n. sp. population investigated from moss of the Greenwich Island, Antarctica. The morphology of Uroleptus (Caudiholosticha) antarctica n. sp. is characterized as follows: 213.0？238.0×67.5？74.5 μm size in vivo; contractile vacuole located slightly above left of mid-body; cortical granules lacking; three frontal and two frontoterminal cirri; five to six transverse cirri; one pretransverse cirri; one right and one left marginal rows; six to seven dorsal kineties; three caudal cirri.