Total Genome Length Research Articles

Characterization of the complete mitochondrial genome of Cynoglossus nanhaiensis (Pleuronectiformes: Cynoglossidae)

In this study, the complete mitochondrial genome of Cynoglossus nanhaiensis was determined. The total length of the mitochondrial genome is 17,130 bp, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The gene rearrangement of tRNAGln gene and control region (CR) were detected, forming a unique gene order of CR-Ile-Gln-Met. Maximum-likelihood and Bayesian inference method are used to perform the phylogenetic analysis, and the result reveals a close relationship between C. nanhaiensis and Cynoglossus itinus.

The complete mitochondrial genomes of three imperiled cyprinid fishes Bonytail (Gila elegans), Rio Grande Silvery Minnow (Hybognathus amarus) and Loach Minnow (Tiaroga cobitis)

Gila elegans, Hybognathus amarus, and Tiaroga cobitis (Family Cyprinidae, Order Cypriniformes) are endemic and endangered fishes in the southwestern United States. We present complete mitochondrial genomes for each species. Each mitochondrion consisted of 13 protein-coding genes, 2 ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and a single control region (D-loop), and gene order was consistent with other cyprinid fishes. Total genome lengths were 16,593 base pairs (bp) for G. elegans, 16,705 bp for H. amarus, and 16,802 for T. cobitis. The GC content in G. elegans and H. amarus was 44%, but higher in T. cobitis at 48%. Phylogenetic trees were generated to confirm relationships inferred via novel mitogenomes, and best-supported trees were consistent with previous research.

The complete chloroplast genome of Musa beccarii

Musa becccarii N.W. Simmonds is one of the most important wild banana species native to Borneo. The chromosome number, 2n = 18, is new to the genus Musa. Wild populations of M. beccarii have been reduced enormously due to massive land clearing for oil palm plantations. In this study, we report the complete chloroplast genome of Musa beccarii by next-generation sequencing (NGS). The total length of the complete chloroplast genome was 168,457 bp, and the overall GC content of the whole genome is 36.8%. The cp genome of Musa beccarii contained a pair of inverted repeat regions of 34,819 bp, which were separated by the large single copy of 88,166bp and the small single copy of 11,059 bp. It encoded 114 genes, including 79 protein-coding genes, 31 tRNA genes, and 4 rRNA ribosomal genes. The most genes occur as a single copy, while 21 gene species occur in double copies. The phylogenetic analysis demonstrateds Musa becccarii formed a single branch among genus Musa. This complete chloroplast genome will provide important information for conservation and identification of species of Musa spp.

Identification, cloning and expression patterns of the genes related to phosphate solubilization in Burkholderia multivorans WS-FJ9 under different soluble phosphate levels

As important plant growth-promoting rhizobacteria, phosphate-solubilizing bacteria (PSB) fix nitrogen, dissolve potassium, promote growth, improve the soil micro-environment, and enhance soil fertility. A high-efficiency PSB strain from the pine tree rhizosphere, Burkholderia multivorans WS-FJ9, was screened in our laboratory. In this study, using a Bio Screener fully automatic microbial growth curve meter to determine the growth of the WS-FJ9 strain in phosphate-removing medium, the growth and mineral phosphate solubilization of WS-FJ9 were measured by Mo-Sb colorimetry and organophosphate-solubilization plate assays. Second-generation sequencing technology was used to obtain genomic information and to analyze possible phosphate decomposition genes. The related expression levels of these genes under different soluble phosphate levels were determined by quantitative real-time PCR. The results showed that WS-FJ9 had strong adaptability and capacity for mineral phosphate solubilization at low soluble phosphate levels, which is characterized by its low soluble phosphate induction and high soluble phosphate inhibition. The amount of solubilized mineral phosphate could exceed 140 mg/L. The total length of the WS-FJ9 genome was 7,497,552 bp after splicing, and the GC content was 67.37%. Eight phosphate-related genes were selected to determine their expression patterns at different soluble phosphate levels. Among them, AP-2, GspE and GspF were only related to organic phosphate, HlyB was only related to inorganic phosphate, and PhoR, PhoA, AP-1 and AP-3 were related to both. The WS-FJ9 strain utilizes multiple pathways for mineral phosphate solubilization, and the solubilization processes of different phosphate sources are interrelated and independent, indicating that the WS-FJ9 strain can adapt to different phosphate source environments and has good potential for future applications.

The complete mitochondrial genomes of two Japanese endemic Satyrinae butterflies, Neope goschkevitschii and Lethe sicelis (Lepidoptera, Nymphalidae)

Neope goschkevitschii and Lethe sicelis are endemic Satyrinae butterflies in mainland Japan, which belongs to the Palearctic realm. In this study, we determined the mitochondrial genomes of these two species. The total length of the mitochondrial genome was 15,286 bp and 15,196 bp for N. goschkevitschii and L. sicelis, respectively, and both mitochondrial genomes were extremely AT-rich. Phylogenetic analysis revealed each of these species was closely related to a member of the same genus, respectively.

Phylogenetic analysis of the complete chloroplast genome of Gracilaria vermiculophylla

In this study, we sequenced and annotated the complete chloroplast genome of Gracilaria vermiculophylla (GenBank accession number: MN853882). The total length of the chloroplast genome of G. vermiculophylla is 180,262 bp, including 191 protein-encoding genes, 30 tRNA genes and 3 rRNA genes. The phylogenetic tree, which is based on core genes, shows that G. vermiculophylla clustered into the Gracilaria clade and has close genetic relationships with algae Gracilaria tenuistipitata and Gracilaria changii. These data will enable a better understanding of the phylogenetic status of G. vermiculophylla.

The complete mitochondrial genome and phylogenetic analysis of Hiatella sp. J (Mollusca: Hiatellidae)

The genus Hiatella is one of most abundant and widespread marine bivalves. To date, its intra-generic phylogeny remains disputed and mitogenome information is therefore much needed. Here, we first report the complete circular mitogenome of Hiatella sp. J that is distributed in the coast of Asia Pacific. The total length of this mitochondrial genome is 21,233 base pairs. It consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a major noncoding region (MNR). Phylogenetic analysis of COI from 25 species (Hiatellidae) revealed that the Hiatella sp. J was closely related to Asian Hiatella in the family Hiatellidae. This Hiatella mitogenome provides new molecular data for the further taxonomic and phylogenetic studies of the genus Hiatella of marine bivalves.

The complete mitochondrial genome of the vent snail Phymorhynchus sp. (Gastropoda: Raphitomidae)

We first determined the complete mitochondrial genome of Phymorhynchus sp. in this study. The total length of the mitochondrial genome of Phymorhynchus sp. was 15,631 bp, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 no-control region. Phylogenetic analysis indicated that Phymorhynchus sp. was most closely related to the Typhlosyrinx sp., another species in the family Raphitomidae.

The complete chloroplast genome sequence of Ulmus glabra ‘Pendula’ (Ulmaceae)

In this study, the whole chloroplast genome of Ulmus glabra ‘Pendula’ was sequenced, assembled, annotated and characterized for the first time. The results showed that the total length of the chloroplast genome of U. glabra ‘Pendula’ was 159,305 bp and the GC content was 35.58%. It had a circular tetrad structure of the chloroplast genome of typical angiosperms, including a large single-copy (LSC) with length of 87,916 bp, a small single-copy (SSC) with length of 18,693 bp, and a pair of inverted repeat sequence (IRs) of 26,348 bp. A total of 131 genes were identified, including 86 protein coding genes, 37 tRNA genes, and 8 rRNA genes. Based on the whole chloroplast genome sequence, the phylogenetic trees of 14 plants in U. glabra ‘Pendula’ and NCBI database were constructed, and the phylogenetic position of U. glabra ‘Pendula’ in Ulmaceae was identified. The results provided important information for the identification of genetic relationship of U. glabra ‘Pendula’, and will also promote the functional analysis of genes related to agronomic traits controlled by the chloroplast genome of U. glabra ‘Pendula’.

The complete chloroplast genome and phylogenetic analysis of Gentiana manshurica Kitag from China

Gentiana manshurica Kitag is a perennial medicinal plant with high economic value. In this study, we first reported the complete chloroplast (cp) genome of G. manshurica. The total length of the cp genome was 149,185 bp in length, consisting of a large single-copy (LSC) region of 81,347 bp, a small single-copy (SSC) region of 17,268 bp, and a pair of inverted repeats (IRs) regions of 25,285 bp each. The cp genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content was 37.61%. The phylogenetic analysis indicated that the G. manshurica belongs to the tribe Gentianeae, and showed a close relationship with other Gentiana species.

Characterization of the complete chloroplast genome of Caesalpinia sappan L. (Leguminosae)

Caesalpinia sappan L. is a widely cultivated medicinal plant. As a first report in this genus, we presented the complete chloroplast genome of C. sappan using genome skimming of paired-end NGS data. The total length of the chloroplast genome was 160,192 bp and contained a typical quadripartite structure including one large single-copy (LSC) region (89,726 bp), one small single copy (SSC) region (18,358 bp) and a pair of inverted repeats (IR) regions (26,054 bp). The GC content of this genome was 36.0%. The whole genome contained 127 genes including 83 protein-coding genes, 36 tRNA genes, and eight rRNA genes. ML analysis revealed C. sappan was closely related to Haematoxylum brasiletto with strong bootstrap values belonging to the subfamily Caesalpinioideae of Leguminosae.

The complete chloroplast genome sequence of Malva verticillata

Malva verticillata, which belongs to the family Malvaceae, is an herb with a wide ecological range and considerable economic and ecological value. herein this study, we determined the complete chloroplast (cp) genome of M. verticillata using Illumina sequencing. The total length of the cpDNA genome was 158,408 bp, including two copies of inverted repeats (IRs, 50,214 bp), a large single copy (LSC, 87,085 bp), and a small single copy (SSC, 21,109 bp). A total of 130 genes were annotated, including 36 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 86 messenger RNA (mRNA) genes. Phylogenetic analysis showed that M. verticillata is closely related to Abelmoschus esculentus, and Hibiscus syriacus among Malvaceae species.

The complete chloroplast genome sequence of the medicinal plant Iphigenia indica Kunth (Liliaceae)

Iphigenia indica is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of I. indica to investigate its phylogenetic relationship in the family Liliaceae. The total length of the chloroplast genome was 158,319 bp, with 30.6% overall GC content, a pair of IRs (inverted repeats) of 28,055 bp was separated by a small single copy (SSC) region of 16,900 bp and a large single copy (LSC) region of 85,309 bp. The cp genome contained 111 genes, including 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Iphigenia was closely related to Asparagus.

The complete mitochondrial genome of water deer in Liaoning, China

We determined the whole mtDNA genome of the water deer (Hydropotes inermis) in Benxi, Liaoning. The total length of the complete mitochondrial genome is 16,355 bp and it consists of 13 protein-coding, 22 tRNA, rRNA genes, and 1 control region (CR). Two overlaps among the 13 protein-coding genes were found: ND4L/ND4 and ND5/ND6. The CR is 928 bp in length. The nucleotide composition is 30.52% A, % 33.38 T, 22.77% G, and 13.32% C.

Complete mitochondrial genome of Brochis multiradiatus

We reported the complete mitochondrial genome yielded by next-generation sequencing of Brochis multiradiatus in this study. The total length of the mitochondrial genome is 16,916 bp, with the base composition of 32.49% A, 25.47% T, 27.12% C, and 14.91% G. It contains 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is the same as that found in the Corydoras. The complete mitochondrial genomes of B. multiradiatus and other 12 species from Siluriformes were used for phylogenetic analysis using neighbor-joining method. The topology demonstrated that all species belong to four genera and are divided into two groups (Siluridae and Callichthyidae), the B. multiradiatus was clustered with genus Corydoras. Brochis multiradiatus’ molecular classification is consistent with the external morphological feature results, so the information of the mitogenome could be used for future identification of Brochis.

Complete mitochondrial genome of Scincella modesta (Squamata: Scincidae)

The first complete mitochondrial genome sequence was determined for an oviparous lizard, Scincella modesta (Scincella, Scincidae). The total length of the complete mitochondrial genome was 17,511 bp, encodes 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and 2 non-coding regions. The overall base composition of S. modesta is A: 31.9%, T: 27.2%, G: 14.5%, and C: 26.5%. Most of the S. modesta mitochondrial genes are encoded on the H-strand except for the ND6 gene and eight tRNA genes, which are encoded on the L-strand. Mrbayes and ML tree based on 13 protein-coding genes indicated that S. vandenburghi is the sister group of the S. modesta within the genus Scincella. The complete mitogenome sequence of S. modesta provided fundamental data for resolving phylogenetic and genetic problems related to genus Scincella.

The complete chloroplast genome of Grateloupia turuturu Yamada

In this study, we sequenced and annotated the complete chloroplast genome of Grateloupia turuturu Yamada (GenBank accession number: MN853877). The total length of the chloroplast genome is 188,547 bps, including 196 protein-encoding genes, 23 tRNA genes and 3 rRNA. The complete chloroplast genome of G. turuturu is 30.68% C + G, which is lower than that of A + T. The phylogenetic tree, which is based on core genes, shows that G. turuturu is clustered into the Grateloupia clade and has close genetic relationships with algae Grateloupia filicina and Grateloupia taiwanensis. These data will provide more information to understand the phylogenetic status of G. turuturu.

Complete mitochondrail genome of Corydoras agassizii

We reported the complete mitochondrial genome yielded using next-generation sequencing of Corydoras agassizii in this study. The total length of the mitochondrial genome is 16,562 bp, with the base composition of 32.6% A, 25.9% T, 26.8% C, and 14.7% G, in several. It contains two rRNA genes, 22 tRNA genes, 13 protein-coding genes, and a 945 bp non-coding control region (D-loop region). The sequence of these genes is consistent with that found in the Siluriformes. The complete mitogenomes of C. agassizii and other 17 species of fish were constructed by phylogenetic analysis using Neighbour-Joining method. The topological structure indicated that species participating in the analysis belong to three groups (Siluridae, Loricariidae, and Callichthyidae) of nine genera, and the C. agassizii was clustered with other species from genus Corydoras. The external morphological characteristics of C. agassizii are consistent with the results of molecular classification, so the mitogenome can be used to identify Corydoras species in the future.

The complete chloroplast genome of Swertia tetraptera and phylogenetic analysis

Swertia tetraptera, native to the Qinghai-Tibetan Plateau, is an important traditional Chinese medicine. Although researchers have done a lot of work on it, the phylogenetic position of S. tetraptera within Swertia has still not been solved. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In present study, we determined the complete chloroplast genome sequences for S. tetraptera using IIumina sequencing. The total length of the complete chloroplast genome of S. tetraptera is 152,840 bp, of which the GC content is 37.95%. The genome encodes 130 functional genes, including 85 protein-coding genes, 37 tRNA, and 8 rRNA. Phylogenetic analysis suggested that S. tetraptera forms monophyletic group with Halenia corniculata which shows closed relationship with the Halenia.

The complete chloroplast genome sequence of an alpine wildflower, Philadelphus calvescens (Rehd.) S. M. Hwang (Saxifragaceae)

Philadelphus calvescens, belonging to the family Saxifragaceae, is a beautiful shrub with white fragrant flowers which is widely distributed in southwest China. In this study, we sequenced the complete chloroplast (cp) genome of P. calvescens to investigate its phylogenetic relationship in Saxifragaceae. Total length of the cpDNA genome was 157,237 bp, consisting of a large single copy (LSC) region of 86,481 bp, a small single copy (SSC) region of 18,728 bp, and a pair of inverted repeat regions (IRs, 26,014 bp). The genome contained 114 genes, namely 79 protein-coding genes, 31 tRNA genes, and 4 rRNA. The overall GC content was 37.8%. Phylogenetic analysis suggested that Philadelphus was closely related to Deutzia. The present study was the first report on complete cp genome of Philadelphus so it could afford important genetic information for further researches on the genus and related genera.