PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data.

"organism sra accession sequencing data (gbp) estimated genome coverage (x) ncbi released mitogenome size (bp) assembled size of this study (bp) accession number pohlia nutans crr383826 a 31 16 44 63 99 864 99 733 nc_046778 b lycopodium japonicum srr24785435 c 2 4 0 59 454 458 or046024 d taxus chinensis srr14756467 e 17 66 1 72 469 770 op177687 d juncus effusus err8282830 e 22 55 100 45 519 026 op177680 d luzula sylvatica err8705854 e 4 74 4 25 633 359 op177679 d arabidopsis thaliana crr302668 a 22 9 191 31 367 808 367 810 nc_037304 b amaranthus tricolor crr511440 a 25 1 53 86 382 432 op177683-85 d cuscuta europaea err9250942 e 25 9 26 54 406 647 406 648 bk059238 b helianthus annuus srr14782853 e 12 82 4 26 300 945 300 887 nc_023337 b jasminum sambac srr17758539 e 43 2 85 19 508 930 op177681 d malus domestica err6939264 e 9 39 13 35 396 947 396 949 nc_018554 b populus trichocarpa srr22064349 c 6 96 16 03 803 673 mz826271-73 d salix wilsonii srr21570388 c 10 26 29 48 711 456 nc_064688 d a downloaded from gsa b publicly available at ncbi c sequenced in this study d submitted to ncbi in this study e downloaded from sra.; the sequencing data of p trichocarpa and m domestica have been submitted to the ncbi sra repository under the accession numbers srr24785916 and srr24789033 respectively.; the pacbio hifi sequencing data of l japonicum p trichocarpa and s wilsonii have been submitted to the ncbi sequence read archive (sra) repository under srr24785435 srr3204721 and srr21570388 respectively.; the illumina sequencing data of the purified mtdna of p trichocarpa and m domestica have been deposited in the sra repository under srr24785916 and srr24789033 respectively."

"the source code for pmat is available at https://github com/bichangwei/pmat .; all listed python scripts are available at https://github com/bichangwei/pmat .; the scripts of pmat are available at https://github com/bichangwei/pmat ."

"Conflict of interest The authors declare no conflicts of interest."

"The work was supported by the National Key Research and Development Plan of China (2021YFD2200202) and the Key Research and Development Project of Jiangsu Province, China (BE2021366). The work was also supported by the Natural Science Foundation of Jiangsu Province (BK20220414), the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province (22KJB220003), the National Natural Science Foundation of China (31901331), and the Innovation Program of Chinese Academy of Agricultural Sciences. We thank Dr Weishu Fan from Kunming Institute of Botany for providing the sample of Lycopodium japonicum."