Reply to Redmond and McLysaght: Uncertainty in the origin of amphioxus IRBP homologs.
Reply to Redmond and McLysaght: Uncertainty in the origin of amphioxus IRBP homologs.
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DOI：
10.1073/pnas.2310867120
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发表时间：
2023-08-22
影响因子：
11.1
通讯作者：
Daugherty, Matthew D.
中科院分区：
文献类型：
--
作者：
Kalluraya, Chinmay A.;Weitzel, Alexander J.;Tsu, Brian V.;Daugherty, Matthew D.
我们最近报道了脊椎动物视觉周期的关键蛋白——光受体间视黄素结合蛋白（IRBP）起源于细菌基因的水平基因转移（HGT）(3)。虽然不是我们的主要研究重点，但我们也发现了一个独立的HGT事件，该事件产生了真菌IRBP同源物，以及文昌鱼基因组中的IRBP同源物。虽然我们的系统发育分析表明文昌鱼蛋白起源于第三个独立的HGT，但由于以下原因，我们仔细地验证了这一结论。考虑到文文鱼和脊椎动物都是脊索动物(4)，但被囊动物（脊椎动物的姐妹分支）似乎缺乏IRBP同源物，我们考虑了两种进化模型：两个独立的HGT事件产生了脊椎动物IRBP和文文鱼IRBP同源物，或者一个单一的HGT事件发生在脊索动物祖先中，IRBP随后在被囊动物中丢失(3)。为了验证这些场景，我们使用全长和单个结构域比对、不同的序列数量、不同的系统发育软件和不同的氨基酸取代模型进行了多种系统发育分析。所有这10项分析都表明文昌鱼和脊椎动物的IRBP同源物起源于不同的HGT事件(3)。我们还发现在脊椎动物和文昌鱼进化枝之间没有共享的内含子或synsyny，尽管每个进化枝中都有共享的内含子和synsyny(3)。然而，我们仍然对单一HGT成为脊索动物祖先的可能性持开放态度(3)，因为如果没有额外的物种代表，系统发育树的深分支很难解决（5,6）。在他们的信(7)中，Redmond和mclysight的目标是通过重新分析我们的序列比对来明确地解决脊椎动物和文昌鱼IRBP同源物的相关性。在一项分析中，他们观察到文昌鱼和脊椎动物IRBP同源物的系统发育分离[图1A(7)]，与我们的8项全长分析一致。在他们的第二次分析中，他们使用了我们对单个IRBP结构域的比对，
We recently reported that interphotoreceptor retinoidbinding protein (IRBP), a key protein in the vertebrate visual cycle (1, 2), originated from the horizontal gene transfer (HGT) of a bacterial gene (3). Although not our primary focus, we also identified an independent HGT event that gave rise to fungal IRBP homologs, as well as IRBP homologs in amphioxus genomes. While our phylogenetic analyses suggested the amphioxus proteins originated as a third independent HGT, we were careful to qualify this conclusion for reasons described below.Given that amphioxus and vertebrates are both chordates (4), but that tunicates (the sister clade to vertebrates) appear to lack IRBP homologs, we considered two evolutionary models: either two independent HGT events gave rise to vertebrate IRBP and amphioxus IRBP homologs or a single HGT event occurred in the chordate ancestor and IRBP was subsequently lost in tunicates (3). To robustly test these scenarios, we performed multiple phylogenetic analyses using full-length and individual domain alignments, different number of sequences, different phylogenetic software, and different amino acid substitution models. All 10 of these analyses indicated that amphioxus and vertebrate IRBP homologs originated from separate HGT events (3). We also found no shared introns or synteny between the vertebrate and amphioxus clades despite shared introns and synteny within each clade (3). However, we remained open to the possibility of a single HGT into a chordate ancestor (3), as deep branches in phylogenetic trees can be difficult to resolve without additional species representatives (5, 6). In their letter (7), Redmond and McLysaght aim to definitively address the relatedness of vertebrate and amphioxus IRBP homologs by reanalyzing our sequence alignments. In one analysis, they observed phylogenetic separation of amphioxus and vertebrate IRBP homologs [figure 1A (7)], consistent with our eight full-length analyses. In their second analysis, they use our alignment of individual IRBP domains,
影响因子：
64.8
作者：
Simakov O;Kawashima T;Marlétaz F;Jenkins J;Koyanagi R;Mitros T;Hisata K;Bredeson J;Shoguchi E;Gyoja F;Yue JX;Chen YC;Freeman RM Jr;Sasaki A;Hikosaka-Katayama T;Sato A;Fujie M;Baughman KW;Levine J;Gonzalez P;Cameron C;Fritzenwanker JH;Pani AM;Goto H;Kanda M;Arakaki N;Yamasaki S;Qu J;Cree A;Ding Y;Dinh HH;Dugan S;Holder M;Jhangiani SN;Kovar CL;Lee SL;Lewis LR;Morton D;Nazareth LV;Okwuonu G;Santibanez J;Chen R;Richards S;Muzny DM;Gillis A;Peshkin L;Wu M;Humphreys T;Su YH;Putnam NH;Schmutz J;Fujiyama A;Yu JK;Tagawa K;Worley KC;Gibbs RA;Kirschner MW;Lowe CJ;Satoh N;Rokhsar DS;Gerhart J
通讯作者：
Gerhart J
视网膜健康和疾病中的球类视内素结合蛋白（IRBP）。
影响因子：
5.3
作者：
Zeng S;Zhang T;Madigan MC;Fernando N;Aggio-Bruce R;Zhou F;Pierce M;Chen Y;Huang L;Natoli R;Gillies MC;Zhu L
通讯作者：
Zhu L
DOI：
10.1073/pnas.2214815120
发表时间：
2023-04-18
影响因子：
11.1
作者：
Kalluraya, Chinmay A.;Weitzel, Alexander J.;Tsu, Brian V.;Daugherty, Matthew D.
通讯作者：
Daugherty, Matthew D.