Van de Paer Céline, Hong-Wa Cynthia, Jeziorski Céline, Besnard Guillaume
CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 Route de Narbonne, 31062 Toulouse, France.
Claude E. Phillips Herbarium, Delaware State University, 1200 N Dupont Hwy Dover, DE 19901-2277, USA.
Gene. 2016 Dec 15;594(2):197-202. doi: 10.1016/j.gene.2016.09.007. Epub 2016 Sep 4.
The recent developments in high-throughput DNA sequencing allowed major advances in organelle genomics. Assembly of mitochondrial genomes (hereafter mitogenomes) in higher plants however remains a challenge due to their large size and the presence of plastid-derived regions and repetitive sequences. In this study, we reconstructed the first mitogenome of Oleaceae using a herbarium specimen of the extinct genus Hesperelaea collected in 1875. Paired-end reads produced with the HiSeq technology (shotgun) in a previous study were re-used. With an approach combining reference-guided and de novo assembly, we obtained a circular molecule of 658,522bp with a mean coverage depth of 35×. We found one large repeat (ca. 8kb) and annotated 46 protein-coding genes, 3 rRNA genes and 19 tRNA genes. A phylogeny of Lamiales mitogenomes confirms Oleaceae as sister to a group comprising Lamiaceae, Phyrmaceae and Gesneriaceae. The Hesperelaea mitogenome has lower rates of synonymous and non-synonymous substitution compared to Nicotiana tabacum than other available mitogenomes of Lamiales. To conclude, we show that mitogenome reconstruction in higher plants is possible with shotgun data, even from poorly preserved DNA extracted from old specimens. This approach offers new perspectives to reconstruct plant phylogenies from mitochondrial markers, and to develop functional mitogenomics in Oleaceae.
高通量DNA测序技术的最新进展推动了细胞器基因组学的重大进步。然而，由于高等植物线粒体基因组（以下简称有丝分裂基因组）的规模较大，且存在质体来源区域和重复序列，其组装仍然是一项挑战。在本研究中，我们利用1875年采集的已灭绝属Hesperelaea的一份植物标本重建了木犀科的首个有丝分裂基因组。我们重新利用了之前一项研究中使用HiSeq技术（鸟枪法）产生的双端测序读段。通过结合参考引导组装和从头组装的方法，我们获得了一个长度为658,522bp的环状分子，平均覆盖深度为35倍。我们发现了一个大约8kb的大重复序列，并注释了46个蛋白质编码基因、3个rRNA基因和19个tRNA基因。唇形目有丝分裂基因组的系统发育分析证实，木犀科是包括唇形科、透骨草科和苦苣苔科在内的一个类群的姐妹群。与烟草相比，Hesperelaea有丝分裂基因组的同义替换率和非同义替换率低于其他现有的唇形目有丝分裂基因组。总之，我们表明，即使是从旧标本中提取的保存不佳的DNA，利用鸟枪法数据也能够完成高等植物有丝分裂基因组的重建。这种方法为从线粒体标记重建植物系统发育以及开展木犀科的功能有丝分裂基因组学研究提供了新的视角。
