http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971266
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the South American endemic moss Codriophorus laevigatus (Grimmiaceae) Monika Szczecin´ska1, Jakub Sawicki1,2, Katarzyna Wołosz1, Halina Bednarek-Ochyra3, and Ryszard Ochyra3 Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Poland, 2Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic, and 3Laboratory of Bryology, Institute of Botany, Polish Academy of Sciences, Poland
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/21/15 For personal use only.
1
Abstract
Keywords
The mitogenome of the Codriophorus laevigatus (GenBank accesion number KM506905) has a total length of 106,809 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes.
Codriophorus laevigatus, Grimmiaceae, mitochondrial genome History Received 12 September 2014 Accepted 19 September 2014 Published online 16 October 2014
The genus Codriophorus is one of four segregates of the traditionally conceived genus Racomitrium (Ochyra et al., 2003). It’s widespread moss group which includes only 15 species (Bednarek-Ochyra, 2006). Codriophorus laevigatus is widely distributed but scattered along the western fringes of southern South America in the Nothofagus zone with an isolated occurrence on the Subantarctic island. The species is well defined morphologically (Bednarek-Ochyra, 2006) and genetically (Bednarek-Ochyra et al., 2014; Larraı´n et al., 2013), and it is characterized by a low level of genetic variation in nuclear and chloroplast sequences, which is why it has been selected as a model species for the present study. Total genomic DNA was extracted from one branched individual from the herbarium specimen (KRAM B-190270) using Genomic Mini AX Plant kit (A&A Biotechnology, Gdan´sk, Poland). A genomic library for MiSeq sequencing was developed with the use of the Nextera XT Kit (Illumina, San Diego, CA). Exactly,1 ng DNA was used in the procedure described in the Nextera XT protocol. Genomic libraries were sequenced using the Miseq 600v3 (Illumina, San Diego, CA) cartridge that supported the acquisition of 2 300 bp pair-end reads. The resulting reads were preliminarily assembled using the Velvet de novo assembler implemented in Illumina BaseCloud service. The obtained contigs were mapped in the Orthotrichum speciosum (Sawicki et al., 2014; GenBank accession number JF793314) genome with the use of medium sensitivity settings implemented in Geneious 6.0.1 software (Biomatters, Auckland, New Zealand). The longest mapped contigs of 8–16 kb were used to reconstruct the C. laevigatus mitogenome. All pair-end reads were mapped in the above sequences with the use of a modified medium sensitivity algorithm (with minimum overlap of 100 bp and 99%
Correspondence: Jakub Sawicki, Department of Botany and Nature Protection, Plac Ło´dzki 1, 10-727 Olsztyn, Poland. E-mail: [email protected]
overlap identity) with 100–1000 iterations. Obtained large contigs were assembled de novo using Geneious 6.0.1 default settings. Genome annotation was performed with the Geneious program using extracted annotations from all eight known bryophyte mitogenomes. Codriophorus laevigatus mitogenome (GenBank accession number KM506905) has a total length of 106,809 bp (73 average coverage), the base composition of the genomes was as follow: A-30.1%, T-30.1%, C 19.1%, G 20.6% wit GC content of 39.7%. The mitochondrial genome consists of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA (Table 1). The mitochondrial structure and gene order was similar to other bryophytes. Table 1. Mitogenome gene order of the South American endemic moss C. laevigatus. Start 254 500 2040 10,012 10,556 11,557 12,773 13,199 13,293 14,181 15,126 16,075 18,217 20,477 21,815 22,831 23,027 23,126
End
Length (bp)
Gene name
327 572 10015 10,563 11,080 12,366 12,843 13,272 14,018 14,708 15,956 17,904 20,428 20,548 21,899 22,914 23,097 23,713
74 73 7976 552 525 810 71 74 726 528 831 183 2212 72 85 84 71 588
trnI (CAU) tRNA trnK (UUU) tRNA COX1 ATP4 ATP9 RPS1 trnC (GCA) tRNA trnF (GAA) tRNA RPS2 CCMB CCMC CCMFN CCMFC trnQ (UUG) tRNA trnL (UAG) tRNA trnS (UGA) tRNA trnG (UCC) tRNA RPS4 (continued )
2
M. Szczecin´ska et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/21/15 For personal use only.
Start 24,446 25,597 25,814 25,942 28,527 29,058 30,377 31,058 33,293 34,247 34,619 35,216 40,632 41,363 41,461 41,542 42,713 49,678 51,976 54,566 54,768 55,352 55,750 56,127 57,577 60,205 64,540 69,151 72,150 75,071 79,231 82,253 85,580 85,675 87,047 87,766 88,676 89,117 89,214 93,093 94,491 94,779 96,383 97,628 98,193 100,058 100,367 101,190 102,183
End
Length (bp)
Gene name
25,156 25,670 25,896 28,223 28,787 30,351 30,450 32,784 33,365 34,368 34,691 38,603 41,171 41,435 41,540 41,621 49,049 51,949 54,406 54,637 54,841 55,424 56,130 56,846 58,948 60,810 69,129 70,785 74,755 77,233 81,795 84,949 85,652 86,031 87,119 87,839 88,748 89,189 92,364 94,487 94,772 96,362 96,790 98,188 98,492 100,363 100,735 101,546 106,485
711 74 83 2282 261 1294 74 1727 73 122 73 3388 540 73 80 80 6337 2272 2431 72 74 73 381 720 1372 606 459 1635 2606 2163 2565 2697 73 357 73 74 73 73 3151 1395 282 1584 408 561 300 306 369 357 4303
TATC trnR (UCU) tRNA trnY (GUA) tRNA NAD4L SDH4 SDH3 trnP (UGG) tRNA 18srRNA trnM (CAU) tRNA 5srRNA trnMf (CAU) tRNA 26srRNA RPL10 trnH (GUG) tRNA trnL (CAA) tRNA trnL (UAA) tRNA NAD5 NAD4 NAD2 trnG (GCC) tRNA trnR (ACG) tRNA trnE (UUC) tRNA RPS12 RPS7 ATP6 NAD6 COX2 COX3 NAD1 COB NAD9 ATP1 trnW (CCA) tRNA NAD3 trnV (UAC) tRNA trnD (GUC) tRNA trnA (UGC) tRNA trnT (GGU) tRNA NAD7 RPL2 RPS19 RPS3 RPL16 RPL5 RPS14 RPL6 RPS13 RPS11 ATP9
The informations of the C. leavigatus mitogenome will be useful for other phylogenetic and phyogeography studies. As the first available mitogenome of complex family Grimmiaceae, C. laevigatus mitochondrial genome will be use as reference during assembly of other mitogenomes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was made possible through financial support from the National Centre of Sciences (grant No. N N 303 796 940).
References Bednarek-Ochyra H. (2006). A taxonomic monograph of the moss genus Codriophorus P. Beauv. (Grimmiaceae). Krako´w, Poland: W. Szafer Institute of Botany, Polish Academy of Sciences. Bednarek-Ochyra H, Ochyra R, Sawicki J, Szczecin´ska M. (2014). Bucklandiella seppeltii, a new species of Grimmiaceae from Australasia and its phylogenetic position based on molecular data. T J Bot (in press). Larraı´n J, Quandt D, Stech M, Mun˜oz J. (2013). Lumping or splitting? The case of Racomitrium (Bryophytina: Grimmiaceae). Taxon 62: 1117–32. Ochyra R,Z_arnowiec J, Bednarek-Ochyra H. (2003). Census catalogue of Polish mosses. Biodivers. Poland 3:1–372. Sawicki J, Szczecin´ska M, Kulik T, Gomolin´ska A, Pla´sˇek V. (2014). The complete mitochondrial genome of the epiphytic moss Orthotrichum speciosum. Mitochondrial DNA DOI:10.3109/19401736.2014.961133.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the South American endemic moss Codriophorus laevigatus (Grimmiaceae) Monika Szczecin´ska1, Jakub Sawicki1,2, Katarzyna Wołosz1, Halina Bednarek-Ochyra3, and Ryszard Ochyra3 Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Poland, 2Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic, and 3Laboratory of Bryology, Institute of Botany, Polish Academy of Sciences, Poland
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/21/15 For personal use only.
1
Abstract
Keywords
The mitogenome of the Codriophorus laevigatus (GenBank accesion number KM506905) has a total length of 106,809 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes.
Codriophorus laevigatus, Grimmiaceae, mitochondrial genome History Received 12 September 2014 Accepted 19 September 2014 Published online 16 October 2014
The genus Codriophorus is one of four segregates of the traditionally conceived genus Racomitrium (Ochyra et al., 2003). It’s widespread moss group which includes only 15 species (Bednarek-Ochyra, 2006). Codriophorus laevigatus is widely distributed but scattered along the western fringes of southern South America in the Nothofagus zone with an isolated occurrence on the Subantarctic island. The species is well defined morphologically (Bednarek-Ochyra, 2006) and genetically (Bednarek-Ochyra et al., 2014; Larraı´n et al., 2013), and it is characterized by a low level of genetic variation in nuclear and chloroplast sequences, which is why it has been selected as a model species for the present study. Total genomic DNA was extracted from one branched individual from the herbarium specimen (KRAM B-190270) using Genomic Mini AX Plant kit (A&A Biotechnology, Gdan´sk, Poland). A genomic library for MiSeq sequencing was developed with the use of the Nextera XT Kit (Illumina, San Diego, CA). Exactly,1 ng DNA was used in the procedure described in the Nextera XT protocol. Genomic libraries were sequenced using the Miseq 600v3 (Illumina, San Diego, CA) cartridge that supported the acquisition of 2 300 bp pair-end reads. The resulting reads were preliminarily assembled using the Velvet de novo assembler implemented in Illumina BaseCloud service. The obtained contigs were mapped in the Orthotrichum speciosum (Sawicki et al., 2014; GenBank accession number JF793314) genome with the use of medium sensitivity settings implemented in Geneious 6.0.1 software (Biomatters, Auckland, New Zealand). The longest mapped contigs of 8–16 kb were used to reconstruct the C. laevigatus mitogenome. All pair-end reads were mapped in the above sequences with the use of a modified medium sensitivity algorithm (with minimum overlap of 100 bp and 99%
Correspondence: Jakub Sawicki, Department of Botany and Nature Protection, Plac Ło´dzki 1, 10-727 Olsztyn, Poland. E-mail: [email protected]
overlap identity) with 100–1000 iterations. Obtained large contigs were assembled de novo using Geneious 6.0.1 default settings. Genome annotation was performed with the Geneious program using extracted annotations from all eight known bryophyte mitogenomes. Codriophorus laevigatus mitogenome (GenBank accession number KM506905) has a total length of 106,809 bp (73 average coverage), the base composition of the genomes was as follow: A-30.1%, T-30.1%, C 19.1%, G 20.6% wit GC content of 39.7%. The mitochondrial genome consists of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA (Table 1). The mitochondrial structure and gene order was similar to other bryophytes. Table 1. Mitogenome gene order of the South American endemic moss C. laevigatus. Start 254 500 2040 10,012 10,556 11,557 12,773 13,199 13,293 14,181 15,126 16,075 18,217 20,477 21,815 22,831 23,027 23,126
End
Length (bp)
Gene name
327 572 10015 10,563 11,080 12,366 12,843 13,272 14,018 14,708 15,956 17,904 20,428 20,548 21,899 22,914 23,097 23,713
74 73 7976 552 525 810 71 74 726 528 831 183 2212 72 85 84 71 588
trnI (CAU) tRNA trnK (UUU) tRNA COX1 ATP4 ATP9 RPS1 trnC (GCA) tRNA trnF (GAA) tRNA RPS2 CCMB CCMC CCMFN CCMFC trnQ (UUG) tRNA trnL (UAG) tRNA trnS (UGA) tRNA trnG (UCC) tRNA RPS4 (continued )
2
M. Szczecin´ska et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/21/15 For personal use only.
Start 24,446 25,597 25,814 25,942 28,527 29,058 30,377 31,058 33,293 34,247 34,619 35,216 40,632 41,363 41,461 41,542 42,713 49,678 51,976 54,566 54,768 55,352 55,750 56,127 57,577 60,205 64,540 69,151 72,150 75,071 79,231 82,253 85,580 85,675 87,047 87,766 88,676 89,117 89,214 93,093 94,491 94,779 96,383 97,628 98,193 100,058 100,367 101,190 102,183
End
Length (bp)
Gene name
25,156 25,670 25,896 28,223 28,787 30,351 30,450 32,784 33,365 34,368 34,691 38,603 41,171 41,435 41,540 41,621 49,049 51,949 54,406 54,637 54,841 55,424 56,130 56,846 58,948 60,810 69,129 70,785 74,755 77,233 81,795 84,949 85,652 86,031 87,119 87,839 88,748 89,189 92,364 94,487 94,772 96,362 96,790 98,188 98,492 100,363 100,735 101,546 106,485
711 74 83 2282 261 1294 74 1727 73 122 73 3388 540 73 80 80 6337 2272 2431 72 74 73 381 720 1372 606 459 1635 2606 2163 2565 2697 73 357 73 74 73 73 3151 1395 282 1584 408 561 300 306 369 357 4303
TATC trnR (UCU) tRNA trnY (GUA) tRNA NAD4L SDH4 SDH3 trnP (UGG) tRNA 18srRNA trnM (CAU) tRNA 5srRNA trnMf (CAU) tRNA 26srRNA RPL10 trnH (GUG) tRNA trnL (CAA) tRNA trnL (UAA) tRNA NAD5 NAD4 NAD2 trnG (GCC) tRNA trnR (ACG) tRNA trnE (UUC) tRNA RPS12 RPS7 ATP6 NAD6 COX2 COX3 NAD1 COB NAD9 ATP1 trnW (CCA) tRNA NAD3 trnV (UAC) tRNA trnD (GUC) tRNA trnA (UGC) tRNA trnT (GGU) tRNA NAD7 RPL2 RPS19 RPS3 RPL16 RPL5 RPS14 RPL6 RPS13 RPS11 ATP9
The informations of the C. leavigatus mitogenome will be useful for other phylogenetic and phyogeography studies. As the first available mitogenome of complex family Grimmiaceae, C. laevigatus mitochondrial genome will be use as reference during assembly of other mitogenomes.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was made possible through financial support from the National Centre of Sciences (grant No. N N 303 796 940).
References Bednarek-Ochyra H. (2006). A taxonomic monograph of the moss genus Codriophorus P. Beauv. (Grimmiaceae). Krako´w, Poland: W. Szafer Institute of Botany, Polish Academy of Sciences. Bednarek-Ochyra H, Ochyra R, Sawicki J, Szczecin´ska M. (2014). Bucklandiella seppeltii, a new species of Grimmiaceae from Australasia and its phylogenetic position based on molecular data. T J Bot (in press). Larraı´n J, Quandt D, Stech M, Mun˜oz J. (2013). Lumping or splitting? The case of Racomitrium (Bryophytina: Grimmiaceae). Taxon 62: 1117–32. Ochyra R,Z_arnowiec J, Bednarek-Ochyra H. (2003). Census catalogue of Polish mosses. Biodivers. Poland 3:1–372. Sawicki J, Szczecin´ska M, Kulik T, Gomolin´ska A, Pla´sˇek V. (2014). The complete mitochondrial genome of the epiphytic moss Orthotrichum speciosum. Mitochondrial DNA DOI:10.3109/19401736.2014.961133.
