Mitochondrial Genome and Phylogeny of Aphelenchoides medicagus

doi:10.13560/j.cnki.biotech.bull.1985.2021-0628

Abstract

Abstract:

Aphelenchoides medicagus is a facultative plant-parasitic nematode that may complete its life cycles on various fungi,meanwhile it has weak parasitism on soybean and alfalfa. In presented study,Illumina platform was used to sequence A. medicagus genome in low coverage. Assembly was made by extracting mitochondrial reads and subsequently assembled by the seed sequence. For the AT rich non-coding region,amplification was made using PCR and sequenced by Sanger method. The jointed result from the assembled and amplified sequences revealed the mitochondrial genome of A. medicagus consisted of 14 411 bp nucleotides,including 12 protein coding genes,22 tRNA and 2 rRNA genes after gene annotation. These genes are arranged in same way as those in A. besseyi,Bursaphelenchus xylophilus,and B. mucronatus. The phylogeny analysis using amino acid sequences showed that A. medicagus and A. besseyi clustered together as a sister group,which together with B. xylophilus and B. mucronatus to form a highly supported monophyletic Aphelenchoididae clade. This study demonstrates that low-coverage whole-genome sequencing method can be used to assemble the most of mitochondrial genome,and thus support this technique to be a feasible tool in mitochondrial genome sequencing.

Key words: Aphelenchoides medicagus, Aphelenchoididae, mitochondrial genome, Illumina platform, low-coverage whole-genome sequencing

XUE Qing, DU Hong-rui, XUE Hui-ying, WANG Yi-hao, WANG Xuan, LI Hong-mei. Mitochondrial Genome and Phylogeny of Aphelenchoides medicagus[J]. Biotechnology Bulletin, 2021, 37(7): 98-106.

Figures/Tables 5

References 32

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基因名 Gene name	起始位点 Start	终止位点 Stop	长度 Length/bp	基因间隔 Intergenic space	起始/终止密码子 Start/stop codons
cox1	955	2535	1 581	0	ATT/TAA
trnC（gca）	2534	2587	54	-2
trnM（cat）	2588	2641	54	0
trnD（gtc）	2642	2696	55	0
trnG（tcc）	2697	2751	55	0
cox2	2761	3450	690	9	ATT/TAA
trnH（gtg）	3450	3503	54	-1
rrnL	3505	4415	911	1
nad3	4423	4758	336	7	ATA/TAA
nad5	4842	6347	1 506	83	ATT/TAG
trnA（tgc）	6346	6399	54	-2
trnP（tgg）	6400	6453	54	0
trnV（tac）	6453	6508	56	-1
nad6	6521	6949	429	12	ATT/TAA
nad4L	6952	7180	229	2	TTG/T
trnW（tca）	7181	7236	56	0
trnE（ttc）	7243	7296	54	6
rrnS	7297	7963	667	0
trnS2（tga）	7966	8019	54	2
trnY（gta）	8021	8074	54	1
nad1	8066	8944	879	-9	ATG/TAA
atp6	8944	9543	600	-1	ATT/TAA
trnK（ttt）	9542	9598	57	-2
trnL2（taa）	9599	9653	55	0
trnS1（tct）	9654	9706	53	0
nad2	9720	10536	817	13	ATA/T
trnI（gat）	10546	10604	59	9
trnR（acg）	10601	10654	54	-4
trnQ（ttg）	10655	10708	54	0
trnF（gaa）	10709	10762	54	0
cob	10760	11884	1 125	-3	ATA/TAA
trnL1（tag）	11880	11936	57	-5
cox3	11942	12691	750	5	ATT/TAG
trnN（gtt）	12692	12745	54	0
trnT（tgt）	12746	12800	55	0
nad4	12807	14033	1 227	6	ATA/TAA

基因名 Gene name	起始位点 Start	终止位点 Stop	长度 Length/bp	基因间隔 Intergenic space	起始/终止密码子 Start/stop codons
cox1	955	2535	1 581	0	ATT/TAA
trnC（gca）	2534	2587	54	-2
trnM（cat）	2588	2641	54	0
trnD（gtc）	2642	2696	55	0
trnG（tcc）	2697	2751	55	0
cox2	2761	3450	690	9	ATT/TAA
trnH（gtg）	3450	3503	54	-1
rrnL	3505	4415	911	1
nad3	4423	4758	336	7	ATA/TAA
nad5	4842	6347	1 506	83	ATT/TAG
trnA（tgc）	6346	6399	54	-2
trnP（tgg）	6400	6453	54	0
trnV（tac）	6453	6508	56	-1
nad6	6521	6949	429	12	ATT/TAA
nad4L	6952	7180	229	2	TTG/T
trnW（tca）	7181	7236	56	0
trnE（ttc）	7243	7296	54	6
rrnS	7297	7963	667	0
trnS2（tga）	7966	8019	54	2
trnY（gta）	8021	8074	54	1
nad1	8066	8944	879	-9	ATG/TAA
atp6	8944	9543	600	-1	ATT/TAA
trnK（ttt）	9542	9598	57	-2
trnL2（taa）	9599	9653	55	0
trnS1（tct）	9654	9706	53	0
nad2	9720	10536	817	13	ATA/T
trnI（gat）	10546	10604	59	9
trnR（acg）	10601	10654	54	-4
trnQ（ttg）	10655	10708	54	0
trnF（gaa）	10709	10762	54	0
cob	10760	11884	1 125	-3	ATA/TAA
trnL1（tag）	11880	11936	57	-5
cox3	11942	12691	750	5	ATT/TAG
trnN（gtt）	12692	12745	54	0
trnT（tgt）	12746	12800	55	0
nad4	12807	14033	1 227	6	ATA/TAA