Cladophorales Plastids Sequence Data and Supplementary

Data for article "Stepwise evolutionary transitions in Cladophorales plastid genomes reveals origins of hairpin chromosomes"Files and Folders:Okellya_plastids.fasta - fasta file of plastid sequences of Okellya marina and Okellya sp. SL.18S.fasta - Nuclear 18S sequences for Okellya marina, Okellya sp. SL, Aegagropila linnaei and Chaetomorpha tokyoensis. Plastid_chromosomes.csv - CSV file of nr90 chromosomes assembled from Aegagropila linnaei and Chaetomorpha tokyoensis. Each row contains the raw assembled sequence of each chromosome (in which ends may be overlapping), non-overlapping unit sequence, GC content and genes detected. Details of start/stop coordinates or if genes detected are functional or pseudogenes are not included.Gene_annotations.csv - CSV file of best gene copies found in Aegagropila linnaei and Chaetmorpha tokyoensis chromosomes, determined by BLASTX e-values to other green algae, and genes present in Okellya marina and Okellya sp. SL plastid genomes. Each row contains the nucleotide sequence, translated sequence, full matching transcript sequence if present (for A. linnaei and C. tokyoensis), chromosome gene copy is found in (for A. linnaei and C. tokyoensis) and relevant notes. Note that exact start codons are uncertain in all species.17_gene_phylogeny - Data for ML phylogeny. AA files were aligned with mafft (--linsi) and trimmed with trimAl (-gt 0.8).Codon_alignments - Data for dN/dS analysis. Some Cladophorales species with partial sequences have been removed. Codon-aware alignments have internal TAG codons changed to NNN. AA files were aligned with mafft (--linsi) and codon-aware alignments made with PAL2NAL (https://www.bork.embl.de/pal2nal/).

论文《枝蕨藻目（Cladophorales）质体基因组的逐步演化转变揭示发夹染色体的起源》配套数据
文件与文件夹如下：
Okellya_plastids.fasta：冈村藻属（Okellya）海洋冈村藻（Okellya marina）及SL菌株冈村藻未定种（Okellya sp. SL）的质体序列FASTA文件
18S.fasta：冈村藻属海洋冈村藻、SL菌株冈村藻未定种、林奈藻（Aegagropila linnaei）及东京毛藻（Chaetomorpha tokyoensis）的核18S序列FASTA文件
Plastid_chromosomes.csv：由林奈藻及东京毛藻组装得到的nr90质体染色体CSV文件。每行包含各染色体的原始组装序列（首尾可能存在重叠）、非重叠单位序列、GC含量及检测到的基因信息，未包含起始/终止坐标细节，也未标注检测到的基因为功能基因还是假基因
Gene_annotations.csv：林奈藻与东京毛藻染色体中最优基因拷贝的CSV注释文件，通过BLASTX比对其他绿藻的E值，以及冈村藻海洋种、SL菌株未定种的质体基因组中存在的基因来确定。每行包含核苷酸序列、翻译后的氨基酸序列、若存在则附带完全匹配的转录本序列（仅适用于林奈藻与东京毛藻）、该基因拷贝所在的染色体信息（仅适用于林奈藻与东京毛藻）及相关备注。需注意所有物种的起始密码子均未明确
17_gene_phylogeny：该目录存放最大似然（ML）系统发育分析相关数据。氨基酸序列文件通过MAFFT的--linsi参数进行多序列比对，再使用trimAl以-gt 0.8参数进行序列修剪
Codon_alignments：该目录存放dN/dS选择压力分析相关数据。已移除部分序列不完整的枝蕨藻目物种。密码子感知比对文件中内部的TAG密码子已替换为NNN。氨基酸序列先通过MAFFT的--linsi参数完成多序列比对，再通过PAL2NAL工具（https://www.bork.embl.de/pal2nal/）生成密码子感知比对文件